| Title: | Single-cell RNAseq cell cluster labelling by reference |
|---|---|
| Description: | After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data). |
| Authors: | Sarah Williams [aut, cre] |
| Maintainer: | Sarah Williams <[email protected]> |
| License: | GPL-3 |
| Version: | 1.23.0 |
| Built: | 2024-07-20 04:57:51 UTC |
| Source: | https://github.com/bioc/celaref |
Produces a table of within-experiment differential expression results (for either query or reference experiment), where each group (cluster) is compared to the rest of the cells.
contrast_each_group_to_the_rest(dataset_se, dataset_name, groups2test = NA, num_cores = 1, n.group = Inf, n.other = n.group * 5)contrast_each_group_to_the_rest(dataset_se, dataset_name, groups2test = NA, num_cores = 1, n.group = Inf, n.other = n.group * 5)
dataset_se |
Summarised experiment object containing count data. Also
requires 'ID' and 'group' to be set within the cell information
(see |
dataset_name |
Short, meaningful name for this dataset/experiment. |
groups2test |
An optional character vector specificing specific groups to check. By default (set to NA), all groups will be tested. |
num_cores |
Number of cores to use to run MAST jobs in parallel. Ignored if parallel package not available. Set to 1 to avoid parallelisation. Default = 1 |
n.group |
How many cells to keep for each group in groupwise comparisons. Default = Inf |
n.other |
How many cells to keep from everything not in the group. Default = n.group * 5 |
Note that this function is slow, because it runs the differential expression. It only needs to be run once per dataset though (unless group labels change). Having package parallel installed is highly recomended.
If this function runs out of memory, consider specifying n.group and n.other to run on a subset of cells (taken from each group, and proportionally from the rest for each test). Alternatively use subset_cells_by_group to subset dataset_se for each group independantly.
Both reference and query datasets should be processed with this function.
The tables produced by this function (usually named something like de_table.datasetname) contain summarised results of MAST results. Each group is compared versus cells in the group, versus not in the group, (Ie. always a 2-group contrast, other groups information is ignored). As per MAST reccomendataions, the proportion of genes seen in each cell is included in the model.
A tibble the within-experiment de_table (differential expression table). This is a core summary of the individual experiment/dataset, which is used for the cross-dataset comparisons.
The table feilds won't neccesarily match across datasets, as they include cell annotations information. Important columns (used in downstream analysis) are:
Gene identifier
Inner (conservative) 95% confidence interval of log2 fold-change.
Multiple hypothesis corrected p-value (using BH/FDR method)
Cells from this group were compared to everything else
Significnatly differentially expressed (fdr < 0.01), with a positive fold change?
Rank position (within group), ranked by CI inner, highest to lowest.
Rank scaled 0(top most overrepresented genes in group) - 1(top most not-present genes)
Name of dataset/experiment
de_table.demo_query <- contrast_each_group_to_the_rest( demo_query_se, "a_demo_query") de_table.demo_ref <- contrast_each_group_to_the_rest( demo_ref_se, "a_demo_ref", num_cores=2)de_table.demo_query <- contrast_each_group_to_the_rest( demo_query_se, "a_demo_query") de_table.demo_ref <- contrast_each_group_to_the_rest( demo_ref_se, "a_demo_ref", num_cores=2)
This function loads and processes microarray data (from purified cell populations) that can be used as a reference.
contrast_each_group_to_the_rest_for_norm_ma_with_limma(norm_expression_table, sample_sheet_table, dataset_name, sample_name, group_name = "group", groups2test = NA, extra_factor_name = NA, pval_threshold = 0.01)contrast_each_group_to_the_rest_for_norm_ma_with_limma(norm_expression_table, sample_sheet_table, dataset_name, sample_name, group_name = "group", groups2test = NA, extra_factor_name = NA, pval_threshold = 0.01)
norm_expression_table |
A logged, normalised expression table. Any filtering (removal of low-expression probes/genes) |
sample_sheet_table |
Tab-separated text file of sample information. Columns must have names. Sample/microarray ids should be listed under sample_name column. The cell-type (or 'group') of each sample should be listed under a column group_name. |
dataset_name |
Short, meaningful name for this dataset/experiment. |
sample_name |
Name of sample_sheet_table with sample ID |
group_name |
Name of sample_sheet_table with group/cell-type. Default = "group" |
groups2test |
An optional character vector specificing specific groups to check. By default (set to NA), all groups will be tested. |
extra_factor_name |
Optionally, an extra cross-group factor (as column name in sample_sheet_table) to include in the model used by limma. E.g. An individual/mouse id. Refer limma docs. Default = NA |
pval_threshold |
For reporting only, a p-value threshold. Default = 0.01 |
Sometimes there are microarray studies measureing purified cell populations that would be measured together in a single-cell sequenicng experiment. E.g. comparing PBMC scRNA to FACs-sorted blood cell populations. This function will process microarray data with limma and format it for comparisions.
The microarray data used should consist of purified cell types from /emphone single study/experiment (due to batch effects). Ideally just those cell-types expected in the scRNAseq, but the method appears relatively robust to a few extra cell types.
Note that unlike the single-cell workflow there are no summarisedExperiment
objects (they're not really comparable) - this function reads data and
generates a table of within-dataset differentential expression contrasts in
one step. Ie. equivalent to the output of
contrast_each_group_to_the_rest.
Also, note that while downstream functions can accept the microarray-derived data as query datasets, its not really intended and assumptions might not hold (Generally, its known what got loaded onto a microarray!)
The (otherwise optional) 'limma' package must be installed to use this function.
A tibble, the within-experiment de_table (differential expression table)
contrast_each_group_to_the_rest is the
funciton that makes comparable output on the scRNAseq data (dataset_se
objects).
Limma Limma package for differential expression.
Other Data loading functions: load_dataset_10Xdata,
load_se_from_tables
contrast_each_group_to_the_rest_for_norm_ma_with_limma( norm_expression_table=demo_microarray_expr, sample_sheet_table=demo_microarray_sample_sheet, dataset_name="DemoSimMicroarrayRef", sample_name="cell_sample", group_name="group") ## Not run: contrast_each_group_to_the_rest_for_norm_ma_with_limma( norm_expression_table, sample_sheet_table=samples_table, dataset_name="Watkins2009PBMCs", extra_factor_name='description') ## End(Not run)contrast_each_group_to_the_rest_for_norm_ma_with_limma( norm_expression_table=demo_microarray_expr, sample_sheet_table=demo_microarray_sample_sheet, dataset_name="DemoSimMicroarrayRef", sample_name="cell_sample", group_name="group") ## Not run: contrast_each_group_to_the_rest_for_norm_ma_with_limma( norm_expression_table, sample_sheet_table=samples_table, dataset_name="Watkins2009PBMCs", extra_factor_name='description') ## End(Not run)
Internal function to calculate differential expression within an experiment between a specified group and cells not in that group.
contrast_the_group_to_the_rest(dataset_se, the_group, pvalue_threshold = 0.01, n.group = Inf, n.other = n.group * 5)contrast_the_group_to_the_rest(dataset_se, the_group, pvalue_threshold = 0.01, n.group = Inf, n.other = n.group * 5)
dataset_se |
Datast summarisedExperiment object. |
the_group |
group to test |
pvalue_threshold |
Default = 0.01 |
n.group |
How many cells to keep for each group in groupwise comparisons. Default = Inf |
n.other |
How many cells to keep from everything not in the group. Default = n.group * 5 |
This function should only be called by
contrast_each_group_to_the_rest
(which can be passed a single group name if desired). Else 'pofgenes' will
not be defined.
MAST is supplied with log2(counts + 1.1), and zlm called with model '~ TvsR + pofgenes' . The p-values reported are from the hurdle model. FDR is with default fdr/BH method.
A tibble, the within-experiment de_table (differential expression table), for the group specified.
contrast_each_group_to_the_rest
Private function used by contrast_each_group_to_the_rest_for_norm_ma_with_limma
contrast_the_group_to_the_rest_with_limma_for_microarray(norm_expression_table, sample_sheet_table, the_group, sample_name, extra_factor_name = NA, pval_threshold = 0.01)contrast_the_group_to_the_rest_with_limma_for_microarray(norm_expression_table, sample_sheet_table, the_group, sample_name, extra_factor_name = NA, pval_threshold = 0.01)
norm_expression_table |
A logged, normalised expression table. Any filtering (removal of low-expression probes/genes) |
sample_sheet_table |
Tab-separated text file of sample information. Columns must have names. Sample/microarray ids should be listed under sample_name column. The cell-type (or 'group') of each sample should be listed under a column group_name. |
the_group |
Which query group is being tested. |
sample_name |
Name of sample_sheet_table with sample ID |
extra_factor_name |
Optionally, an extra cross-group factor (as column name in sample_sheet_table) to include in the model used by limma. E.g. An individual/mouse id. Refer limma docs. Default = NA |
pval_threshold |
For reporting only, a p-value threshold. Default = 0.01 |
A tibble, the within-experiment de_table (differential expression table), for the group specified.
contrast_each_group_to_the_rest_for_norm_ma_with_limma
public calling function
Limma Limma package for differential expression.
Change the gene IDs in in the supplied datatset_se object to some other id
already present in the gene info (as seen with rowData())
convert_se_gene_ids(dataset_se, new_id, eval_col, find_max = TRUE)convert_se_gene_ids(dataset_se, new_id, eval_col, find_max = TRUE)
dataset_se |
Summarised experiment object containing count data. Also
requires 'ID' and 'group' to be set within the cell information
(see |
new_id |
A column within the feature information (view
|
eval_col |
Which column to use to break ties of duplicate
new_id. Must be a column within the feature information (view
|
find_max |
If false, this will choose the minimal eval_col instead of max. Default = TRUE |
A modified dataset_se - ID will now be new_id, and unique. It will have fewer genes if old ID to new ID was not a 1:1 mapping. The selected genes will be according to the eval col max (or min). should pick the alphabetical first on ties, but could change.
SummarizedExperiment For general doco on the SummarizedExperiment objects.
load_se_from_files For reading data from flat
files (not 10X cellRanger output)
# The demo dataset doesn't have other names, so make some up # (don't do this) dataset_se <- demo_ref_se rowData(dataset_se)$dummyname <- toupper(rowData(dataset_se)$ID) # If not already present, define a column to evaluate, # typically total reads/gene. rowData(dataset_se)$total_count <- rowSums(assay(dataset_se)) dataset_se <- convert_se_gene_ids(dataset_se, new_id='dummyname', eval_col='total_count')# The demo dataset doesn't have other names, so make some up # (don't do this) dataset_se <- demo_ref_se rowData(dataset_se)$dummyname <- toupper(rowData(dataset_se)$ID) # If not already present, define a column to evaluate, # typically total reads/gene. rowData(dataset_se)$total_count <- rowSums(assay(dataset_se)) dataset_se <- convert_se_gene_ids(dataset_se, new_id='dummyname', eval_col='total_count')
Small example dataset that is the output of contrast_each_group_to_the_rest. It contains the results of each group compared to the rest of the sample (ie within sample differential expression)
de_table.demo_queryde_table.demo_query
An object of class data.frame with 800 rows and 13 columns.
An example de_table from contrast_each_group_to_the_rest (for demo query dataset)
Small example dataset that is the output of contrast_each_group_to_the_rest. It contains the results of each group compared to the rest of the sample (ie within sample differential expression)
de_table.demo_refde_table.demo_ref
An object of class data.frame with 800 rows and 13 columns.
An example de_table from contrast_each_group_to_the_rest (for demo ref dataset)
Sample sheet table listing each cell, its assignd cluster/group, and any other information that might be interesting (replicate, individual e.t.c)
demo_cell_info_tabledemo_cell_info_table
An object of class data.frame with 515 rows and 4 columns.
An example cell info table
Counts matrix for a small, demo example datasets. Raw counts of reads per gene (row) per cell (column).
demo_counts_matrixdemo_counts_matrix
An object of class matrix with 200 rows and 514 columns.
An example counts matrix.
Extra table of gene-level information for the demo example dataset. Can contain anything as long as theres a unique gene id.
demo_gene_info_tabledemo_gene_info_table
An object of class data.frame with 200 rows and 2 columns.
An example table of genes.
Microarray-style expression table for the demo example dataset. Rows are genes, columns are samples, as per counts matrix.
demo_microarray_exprdemo_microarray_expr
An object of class matrix with 200 rows and 20 columns.
An example table of (fake) microarray data.
Microarray sample sheet table for the demo example dataset. Contains array identifiers, their group and any other information that could be useful.
demo_microarray_sample_sheetdemo_microarray_sample_sheet
An object of class grouped_df (inherits from tbl_df, tbl, data.frame) with 20 rows and 2 columns.
An example microarray sample sheet
A summarisedExperiment object loaded from demo info tables, for a query set.
demo_query_sedemo_query_se
An object of class SummarizedExperiment with 200 rows and 485 columns.
An example summarised experiment (for demo query dataset)
A summarisedExperiment object loaded from demo info tables, for a reference set.
demo_ref_sedemo_ref_se
An object of class SummarizedExperiment with 200 rows and 515 columns.
An example summarised experiment (for demo reference dataset)
Internal function to find if there are significant difference between the distribitions, when there are multiple match groups.
find_within_match_differences(de_table.ref.marked, matches, the_test_group, the_test_dataset, the_ref_dataset, the_pval)find_within_match_differences(de_table.ref.marked, matches, the_test_group, the_test_dataset, the_ref_dataset, the_pval)
de_table.ref.marked |
see make_ref_similarity_names_for_group |
matches |
see make_ref_similarity_names_for_group |
the_test_group |
see make_ref_similarity_names_for_group |
the_test_dataset |
see make_ref_similarity_names_for_group |
the_ref_dataset |
see make_ref_similarity_names_for_group |
the_pval |
see make_ref_similarity_names_for_group |
For use by make_ref_similarity_names_for_group
String of within match differences
make_ref_similarity_names_for_group
get_counts_index is an internal utility function to find out where
the counts are (if anywhere.). Stops if there's no assay called 'counts',
(unless there is only a single unnamed assay).
get_counts_index(n_assays, assay_names)get_counts_index(n_assays, assay_names)
n_assays |
How many assays are there? ie: length(assays(dataset_se)) |
assay_names |
What are the assays called? ie: names(assays(dataset_se)) |
The index of an assay in assays called 'counts', or, if there's just the one unnamed assay - happily assume that that is counts.
Given a fold-change, and high and low confidence interval (where lower < higher), pick the innermost/most conservative one.
get_inner_or_outer_ci(fc, ci.hi, ci.lo, get_inner = TRUE)get_inner_or_outer_ci(fc, ci.hi, ci.lo, get_inner = TRUE)
fc |
Fold-change |
ci.hi |
Higher fold-change CI (numerically) |
ci.lo |
smaller fold-change CI (numerically) |
get_inner |
If TRUE, get the more conservative inner CI, else the bigger outside one. |
inner or outer CI from ci.hi or ci.low
Internal function that wraps limma topTable output but also adds upper and lower confidence intervals to the logFC. Calculated according to https://support.bioconductor.org/p/36108/
get_limma_top_table_with_ci(fit2, the_coef, ci = 0.95)get_limma_top_table_with_ci(fit2, the_coef, ci = 0.95)
fit2 |
The fit2 object after calling eBayes as per standard limma workflow. Ie object that topTable gets called on. |
the_coef |
Coeffient. As passed to topTable. |
ci |
Confidence interval. Number between 0 and 1, default 0.95 (95%) |
Output of topTable, but with the (95 for the logFC.
contrast_the_group_to_the_rest_with_limma_for_microarray
Calling function.
Internal function to grab a table of the matched group(s).
get_matched_stepped_mwtest_res_table(mwtest_res_table.this, the_pval)get_matched_stepped_mwtest_res_table(mwtest_res_table.this, the_pval)
mwtest_res_table.this |
Combined output of
|
the_pval |
Pvalue threshold |
For use by make_ref_similarity_names_for_group
Stepped pvalues string
make_ref_similarity_names_for_group
Internal function to get reference group similarity contrasts for an individual query qroup.
get_ranking_and_test_results(de_table.ref.marked, the_test_group, the_test_dataset, the_ref_dataset, num_steps, pval = 0.01)get_ranking_and_test_results(de_table.ref.marked, the_test_group, the_test_dataset, the_ref_dataset, num_steps, pval = 0.01)
de_table.ref.marked |
|
the_test_group |
The group to calculate the stats on. |
the_test_dataset |
|
the_ref_dataset |
|
num_steps |
|
pval |
For use by make_ref_similarity_names_using_marked, see that function for parameter details. This function just runs this for a single query group the_test_group
Table of similarity contrast results/assigned names e.t.c for a single group. Used internally for populating mwtest_res_table tables.
make_ref_similarity_names_using_marked
which calls this.
Summarise the comparison of the specified query group against in the comparison in de_table.ref.marked - number of 'top' genes and their median rank in each of the reference groups, with reference group rankings.
get_rankstat_table(de_table.ref.marked, the_test_group)get_rankstat_table(de_table.ref.marked, the_test_group)
de_table.ref.marked |
The output of
|
the_test_group |
Name of query group to test |
A tibble of query group name (test_group), number of 'top' genes (n), reference dataset group (group) with its ranking (grouprank) and the median (rescaled 0..1) ranking of 'top' genes (median_rank).
get_the_up_genes_for_all_possible_groups To
prepare the de_table.ref.marked input.
# Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.demo_query, de_table.demo_ref) get_rankstat_table(de_table.marked.query_vs_ref, "Group3")# Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.demo_query, de_table.demo_ref) get_rankstat_table(de_table.marked.query_vs_ref, "Group3")
Internal function to run a bionomial test of median test rank > 0.5 (random).
get_reciprocal_matches(mwtest_res_table.recip, de_table.recip.marked, the_pval)get_reciprocal_matches(mwtest_res_table.recip, de_table.recip.marked, the_pval)
mwtest_res_table.recip |
Combined output of
|
de_table.recip.marked |
Recriprocal ref vs query de_table.ref.marked |
the_pval |
See make_ref_similarity_names_using_marked |
For use by make_ref_similarity_names_using_marked
List of table of reciprocal matches tested from reference to query.
make_ref_similarity_names_using_marked
Internal function to construct the string of stepped pvalues reported by make_ref_similarity_names_using_marked
get_stepped_pvals_str(mwtest_res_table.this)get_stepped_pvals_str(mwtest_res_table.this)
mwtest_res_table.this |
Combined output of
|
For use by make_ref_similarity_names_for_group
Stepped pvalues string
make_ref_similarity_names_for_group
For the most overrepresented genes of each group in the test dataset, get their rankings in all the groups of the reference dataset.
get_the_up_genes_for_all_possible_groups(de_table.test, de_table.ref, rankmetric = "TOP100_LOWER_CI_GTE1", n = 100)get_the_up_genes_for_all_possible_groups(de_table.test, de_table.ref, rankmetric = "TOP100_LOWER_CI_GTE1", n = 100)
de_table.test |
A differential expression table of the query
experiment, as generated from
|
de_table.ref |
A differential expression table of the reference
dataset, as generated from
|
rankmetric |
Specifiy ranking method used to pick the 'top' genes. The default 'TOP100_LOWER_CI_GTE1' picks genes from the top 100 overrepresented genes (ranked by inner 95 work best for distinct cell types (e.g. tissue sample.). 'TOP100_SIG' again picks from the top 100 ranked genes, but requires only statistical significance, 95 clusters (e.g. PBMCs). |
n |
For tweaking maximum returned genes from different ranking methods. Will change the p-values! Suggest leaving as default unless you're keen. |
This is effectively a subset of the reference data, 'marked' with the 'top' genes that represent the groups in the query data. The distribution of the rescaled ranks of these marked genes in each reference data group indicate how similar they are to the query group.
This function is simply a conveinent wrapper for
get_the_up_genes_for_group that merges output for
each group in the query into one table.
de_table.marked This will alsmost be a subset of de_table.ref, with an added column test_group set to the query groups, and test_dataset set to test_dataset_name.
If nothing passes the rankmetric criteria, a warning is thrown and NA is returned. (This can be a genuine inability to pick out the representative 'up' genes, or due to some problem in the analysis)
get_the_up_genes_for_group Function for
testing a single group.
de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.test=de_table.demo_query , de_table.ref=de_table.demo_ref )de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.test=de_table.demo_query , de_table.ref=de_table.demo_ref )
For the most overrepresented genes of the specified group in the test dataset, get their rankings in all the groups of the reference dataset.
get_the_up_genes_for_group(the_group, de_table.test, de_table.ref, rankmetric = "TOP100_LOWER_CI_GTE1", n = 100)get_the_up_genes_for_group(the_group, de_table.test, de_table.ref, rankmetric = "TOP100_LOWER_CI_GTE1", n = 100)
the_group |
The group (from the test/query experiment) to examine. |
de_table.test |
A differential expression table of the query
experiment, as generated from
|
de_table.ref |
A differential expression table of the reference
dataset, as generated from
|
rankmetric |
Specifiy ranking method used to pick the 'top' genes. The default 'TOP100_LOWER_CI_GTE1' picks genes from the top 100 overrepresented genes (ranked by inner 95 work best for distinct cell types (e.g. tissue sample.). 'TOP100_SIG' again picks from the top 100 ranked genes, but requires only statistical significance, 95 clusters (e.g. PBMCs). |
n |
For tweaking maximum returned genes from different ranking methods. Will change the p-values! Suggest leaving as default unless you're keen. |
This is effectively a subset of the reference data, 'marked' with the 'top' genes that represent the group of interest in the query data. The distribution of the rescaled ranks of these marked genes in each reference data group indicate how similar they are to the query group.
de_table.marked This will be a subset of de_table.ref, with an added column test_group set to the_group. If nothing passes the rankmetric criteria, NA.
contrast_each_group_to_the_rest For prepraring the
de_table.* tables.
get_the_up_genes_for_all_possible_groups For running
all query groups at once.
de_table.marked.Group3vsRef <- get_the_up_genes_for_group( the_group="Group3", de_table.test=de_table.demo_query, de_table.ref=de_table.demo_ref)de_table.marked.Group3vsRef <- get_the_up_genes_for_group( the_group="Group3", de_table.test=de_table.demo_query, de_table.ref=de_table.demo_ref)
Internal function to run a bionomial test of median test rank > 0.5 (random).
get_vs_random_pval(de_table.ref.marked, the_group, the_test_group)get_vs_random_pval(de_table.ref.marked, the_group, the_test_group)
de_table.ref.marked |
see make_ref_similarity_names_for_group |
the_group |
Reference group name |
the_test_group |
Test group name #' |
For use by make_ref_similarity_names_for_group
Pvalue result of a binomial test of each 'top gene' being greater than the theoretical random median rank of 0.5 (halfway).
make_ref_similarity_names_for_group
Convenience function to create a SummarizedExperiment object (dataset_se) from a the output of 10X cell ranger pipeline run.
load_dataset_10Xdata(dataset_path, dataset_genome, clustering_set, gene_id_cols_10X = c("ensembl_ID", "GeneSymbol"), id_to_use = gene_id_cols_10X[1])load_dataset_10Xdata(dataset_path, dataset_genome, clustering_set, gene_id_cols_10X = c("ensembl_ID", "GeneSymbol"), id_to_use = gene_id_cols_10X[1])
dataset_path |
Path to the directory of 10X data, as generated by the cellRanger pipeline (versions 2.1.0 and 2.0.1). The directory should have subdirecotires analysis, filtered_gene_bc_matrices and raw_gene_bc_matrices (only the first 2 are read). |
dataset_genome |
The genome that the reads were aligned against, e.g. GRCh38. Check for this as a directory name under the filtered_gene_bc_matrices subdirectory if unsure. |
clustering_set |
The 10X cellRanger pipeline produces several different cluster definitions per dataset. Specify which one to use e.g. kmeans_10_clusters Find them as directory names under analysis/clustering/ |
gene_id_cols_10X |
Vector of the names of the columns in the gene description file (filtered_gene_bc_matrices/GRCh38/genes.csv). The first element of this will become the ID. Default = c("ensembl_ID","GeneSymbol") |
id_to_use |
Column from gene_id_cols_10X that defines the gene
identifier to use as 'ID' in the returned SummarisedExperiment object.
Many-to-one relationships betwen the assumed unique first element of
gene_id_cols_10X and id_to_use will be handled gracefully by
|
This function makes a SummarizedExperiment object in a form that
should work for celaref functions. Specifically, that means it will have an
'ID' feild for genes (view with rowData(dataset_se)), and both
'cell_sample' and 'group' feild for cells (view with
colData(dataset_se)). See parameters for detail.
Additionally, the counts will be an integer matrix (not a
sparse matrix), and the group feild (but not cell_sample
or ID) will be a factor.
The clustering information can be read from whichever cluster is specified, usually there will be several choices.
This funciton is designed to work with output of version 2.0.1 of the cellRanger pipeline, may not work with others (will not work for 1.x).
A SummarisedExperiment object containing the count data, cell info and gene info.
SummarizedExperiment For general doco on the SummarizedExperiment objects.
convert_se_gene_ids describes method for
converting IDs.
Other Data loading functions: contrast_each_group_to_the_rest_for_norm_ma_with_limma,
load_se_from_tables
example_10X_dir <- system.file("extdata", "sim_cr_dataset", package = "celaref") dataset_se <- load_dataset_10Xdata(example_10X_dir, dataset_genome="GRCh38", clustering_set="kmeans_4_clusters", gene_id_cols_10X=c("gene")) ## Not run: dataset_se <- load_dataset_10Xdata('~/path/to/data/10X_pbmc4k', dataset_genome="GRCh38", clustering_set="kmeans_7_clusters") ## End(Not run)example_10X_dir <- system.file("extdata", "sim_cr_dataset", package = "celaref") dataset_se <- load_dataset_10Xdata(example_10X_dir, dataset_genome="GRCh38", clustering_set="kmeans_4_clusters", gene_id_cols_10X=c("gene")) ## Not run: dataset_se <- load_dataset_10Xdata('~/path/to/data/10X_pbmc4k', dataset_genome="GRCh38", clustering_set="kmeans_7_clusters") ## End(Not run)
Create a SummarizedExperiment object (dataset_se) from a count matrix, cell information and optionally gene information.
load_se_from_files is a wrapper for load_se_from_tables that
will read in tables from specified files.
load_se_from_tables(counts_matrix, cell_info_table, gene_info_table = NA, group_col_name = "group", cell_col_name = NA) load_se_from_files(counts_file, cell_info_file, gene_info_file = NA, group_col_name = "group", cell_col_name = NA)load_se_from_tables(counts_matrix, cell_info_table, gene_info_table = NA, group_col_name = "group", cell_col_name = NA) load_se_from_files(counts_file, cell_info_file, gene_info_file = NA, group_col_name = "group", cell_col_name = NA)
counts_matrix |
A tab-separated matrix of read counts for each gene (row) and each cell (column). Columns and rows should be named. |
cell_info_table |
Table of cell information. If there is a column labelled cell_sample, that will be used as the unique cell identifiers. If not, the first column is assumed to be cell identifiers, and will be copied to a new feild labelled cell_sample. Similarly - the clusters of these cells should be listed in one column - which can be called 'group' (case-sensitive) or specified with group_col_name. Minimal data format: <cell_sample> <group> |
gene_info_table |
Optional table of gene information. If there is a column labelled ID, that will be used as the gene identifiers (they must be unique!). If not, the first column is assumed to be a gene identifier, and will be copied to a new feild labelled ID. Must match all rownames in counts_matrix. If omitted, ID wll be generated from the rownames of counts_matrix. Default=NA |
group_col_name |
Name of the column in cell_info_table containing the cluster/group that each cell belongs to. Case-sensitive. Default='group' |
cell_col_name |
Name of the column in cell_info_table containing a cell id. Ignored if cell_sample column is already present. If omitted, (and no cell_sample column) will use first column. Case-sensitive. Default=NA |
counts_file |
A tab-separated file of a matrix of read counts. As per counts_matrix. First column should be gene ID, and top row cell ids. |
cell_info_file |
Tab-separated text file of cell information, as per cell_info_table. Columns must have names. |
gene_info_file |
Optional tab-separated text file of gene information, as per gene_info_file. Columns must have names. Default=NA |
This function makes a SummarizedExperiment object in a form that
should work for celaref functions. Specifically, that means it will have an
'ID' feild for genes (view with rowData(dataset_se)), and both
'cell_sample' and 'group' feild for cells (view with
colData(dataset_se)). See parameters for detail.
Additionally, the counts will be an integer matrix (not a
sparse matrix), and the group feild (but not cell_sample
or ID) will be a factor.
Note that data will be subsetted to cells present in both the counts matrix and cell info, this is handy for loading subsets of cells. However, if gene_info_file is defined, all genes must match exactly.
The load_se_from_files form of this function will run the same
checks, but will read everything from files in one go. The
load_se_from_tables
form is perhaps more useful when the annotations need to be modified (e.g.
programmatically adding a different gene identifier, renaming groups,
removing unwanted samples).
Note that the SummarizedExperiment object can also be created without using these functions, it just needs the cell_sample, ID and group feilds as described above. Since sometimes it might be easier to add these to an existing SummarizedExperiment from upstream analyses.
A SummarisedExperiment object containing the count data, cell info and gene info.
load_se_from_files: To read from files
SummarizedExperiment For general doco on the SummarizedExperiment objects.
Other Data loading functions: contrast_each_group_to_the_rest_for_norm_ma_with_limma,
load_dataset_10Xdata
# From data frames (or a matrix for counts) : demo_se <- load_se_from_tables(counts_matrix=demo_counts_matrix, cell_info_table=demo_cell_info_table) demo_se <- load_se_from_tables(counts_matrix=demo_counts_matrix, cell_info_table=demo_cell_info_table, gene_info_table=demo_gene_info_table) # Or from data files : counts_filepath <- system.file("extdata", "sim_query_counts.tab", package = "celaref") cell_info_filepath <- system.file("extdata", "sim_query_cell_info.tab", package = "celaref") gene_info_filepath <- system.file("extdata", "sim_query_gene_info.tab", package = "celaref") demo_se <- load_se_from_files(counts_file=counts_filepath, cell_info_file=cell_info_filepath) demo_se <- load_se_from_files(counts_file=counts_filepath, cell_info_file=cell_info_filepath, gene_info_file=gene_info_filepath )# From data frames (or a matrix for counts) : demo_se <- load_se_from_tables(counts_matrix=demo_counts_matrix, cell_info_table=demo_cell_info_table) demo_se <- load_se_from_tables(counts_matrix=demo_counts_matrix, cell_info_table=demo_cell_info_table, gene_info_table=demo_gene_info_table) # Or from data files : counts_filepath <- system.file("extdata", "sim_query_counts.tab", package = "celaref") cell_info_filepath <- system.file("extdata", "sim_query_cell_info.tab", package = "celaref") gene_info_filepath <- system.file("extdata", "sim_query_gene_info.tab", package = "celaref") demo_se <- load_se_from_files(counts_file=counts_filepath, cell_info_file=cell_info_filepath) demo_se <- load_se_from_files(counts_file=counts_filepath, cell_info_file=cell_info_filepath, gene_info_file=gene_info_filepath )
Plot a panel of violin plots showing the distribution of the 'top' genes of each of query group, across the reference dataset.
make_ranking_violin_plot(de_table.marked = NA, de_table.test = NA, de_table.ref = NA, log10trans = FALSE, ...)make_ranking_violin_plot(de_table.marked = NA, de_table.test = NA, de_table.ref = NA, log10trans = FALSE, ...)
de_table.marked |
The output of
|
de_table.test |
A differential expression table of the
query experiment,
as generated from |
de_table.ref |
A differential expression table of the
reference dataset,
as generated from |
log10trans |
Plot on a log scale? Useful for distinishing multiple similar, yet distinct cell type that bunch at top of plot. Default=FALSE. |
... |
Further options to be passed to
|
In the plot output, each panel correponsds to a different group/cluster in the query experiment. The x-axis has the groups in the reference dataset. The y-axis is the rescaled rank of each 'top' gene from the query group, within each reference group.
Only the 'top' genes for each query group are plotted, forming the violin plots - each individual gene is shown as a tickmark. Some groups have few top genes, and so their uncertanty can be seen on this plot.
The thick black lines reprenset the median gene rescaled ranking for each query group / reference group combination. Having this fall above the dotted median threshold marker is a quick indication of potential similarity. A complete lack of similarity would have a median rank around 0.5. Median rankings much less than 0.5 are common though (an 'anti-cell-groupA' signature), because genes overrepresented in one group in an experiment, are likely to be relatively 'underrepresented' in the other groups. Taken to an extreme, if there are only two reference groups, they'll be complete opposites.
Input can be either the precomputed de_table.marked object for the
comparison, OR both de_table.test and de_table.ref
differential expression results to compare from
contrast_each_group_to_the_rest
A ggplot object.
get_the_up_genes_for_all_possible_groups To make
the input data.
# Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") # This: make_ranking_violin_plot(de_table.test=de_table.demo_query, de_table.ref=de_table.demo_ref ) # Is equivalent to this: de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.test=de_table.demo_query, de_table.ref=de_table.demo_ref) make_ranking_violin_plot(de_table.marked.query_vs_ref)# Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") # This: make_ranking_violin_plot(de_table.test=de_table.demo_query, de_table.ref=de_table.demo_ref ) # Is equivalent to this: de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.test=de_table.demo_query, de_table.ref=de_table.demo_ref) make_ranking_violin_plot(de_table.marked.query_vs_ref)
Construct some sensible labels or the groups/clusters in the query dataset, based on similarity the reference dataset.
This is a more low level/customisable version of
make_ref_similarity_names, (would usually use that instead).
Suitable for rare cases to reuse an existing de_table.ref.marked
object. Or use a de_table.ref.marked table with more than one dataset
present (discoraged). Or to skip the reciprocal comparison step.
make_ref_similarity_names(de_table.test, de_table.ref, pval = 0.01, num_steps = 5, rankmetric = "TOP100_LOWER_CI_GTE1", n = 100) make_ref_similarity_names_using_marked(de_table.ref.marked, de_table.recip.marked = NA, the_test_dataset = NA, the_ref_dataset = NA, pval = 0.01, num_steps = 5)make_ref_similarity_names(de_table.test, de_table.ref, pval = 0.01, num_steps = 5, rankmetric = "TOP100_LOWER_CI_GTE1", n = 100) make_ref_similarity_names_using_marked(de_table.ref.marked, de_table.recip.marked = NA, the_test_dataset = NA, the_ref_dataset = NA, pval = 0.01, num_steps = 5)
de_table.test |
A differential expression table of the query
experiment, as generated from
|
de_table.ref |
A differential expression table of the reference
dataset, as generated from
|
pval |
Differences between the rescaled ranking distribution of 'top' genes on different reference groups are tested with a Mann-Whitney U test. If they are significantly different, only the top group(s) are reported. It isn't a simple cutoff threshold as it can change the number of similar groups reported. ie. A more stringent pval is more likely to decide that groups are similar - which would result in multiple group reporting, or no similarity at all. Unlikely that this parameter will ever need to change. Default = 0.01. |
num_steps |
After ranking reference groups according to median 'top' gene ranking, how many adjacent pairs to test for differences. Set to 1 to only compare each group to the next, or NA to perform an all-vs-all comparison. Setting too low may means it is possible to miss groups with some similarity to the reported matches (similar_non_match column)). Too high (or NA) with a large number of reference groups could be slow. Default = 5. |
rankmetric |
Specifiy ranking method used to pick the 'top' genes. The default 'TOP100_LOWER_CI_GTE1' picks genes from the top 100 overrepresented genes (ranked by inner 95 work best for distinct cell types (e.g. tissue sample.). 'TOP100_SIG' again picks from the top 100 ranked genes, but requires only statistical significance, 95 clusters (e.g. PBMCs). |
n |
For tweaking maximum returned genes from different ranking methods. |
de_table.ref.marked |
The output of
|
de_table.recip.marked |
Optional. The (reciprocal) output of
|
the_test_dataset |
Optional. A short meaningful name for the experiment. (Should match test_dataset column in de_table.marked). Only needed in a table of more than one dataset. Default = NA. |
the_ref_dataset |
Optional. A short meaningful name for the experiment. (Should match dataset column in de_table.marked). Only needed in a table of more than one dataset. Default = NA. |
This function aims to report a) the top most similar reference group, if there's a clear frontrunner, b) A list of multiple similar groups if they have similar similarity, or c) 'No similarity', if there is none.
Each group is named according to the following rules. Testing for significant (smaller) differences with a one-directional Mann-Whitney U test on their rescaled ranks:
The first (as ranked by median rescaled rank) reference group is significantly more similar than the next: Report first only.
When comparing differences betwen groups stepwise ranked by median rescaled rank - no group is significantly different to its neighbour: Report no similarity
There's no significant differences in the stepwise comparisons of the first N reference groups - but there is a significant difference later on : Report multiple group similarity
There are some further heuristic caveats:
The distribution of top genes in the last (or only) match group is tested versus a theroetical random distribution around 0.5 (as reported in pval_vs_random column). If the distribution is not significantly above random (It is possible in edge cases where there is a skewed dataset and no/few matches), no similarity is reported. The significnat pval column is left intact.
The comparison is repeated reciprocally - reference groups vs the query groups. This helps sensitivity of heterogenous query groups - and investigating the reciprocal matches can be informative in these cases. If a query group doens't 'match' a reference group, but the reference group does match that query group - it is reported in the group label in brackets. e.g. c1:th_lymphocytes(tc_lympocytes). Its even possible if there was no match (and pval = NA) e.g. emphc2:(tc_lymphocytes)
The similarity is formatted into a group label. Where there are multiple similar groups, they're listed from most to least similar by their median ranks.
For instance, a query dataset of clusters c1, c2, c3 and c4 againsts a cell-type labelled reference datatset might get names like: E.g.
c1:macrophage
c2:endotheial|mesodermal
c3:no_similarity
c4:mesodermal(endothelial)
Function make_ref_similarity_names is a convenience wrapper function
for make_ref_similarity_names_from_marked. It accepts two 'de_table'
outputs of function contrast_each_group_to_the_rest to compare
and handles running
get_the_up_genes_for_all_possible_groups.
Sister function make_ref_similarity_names_from_marked may (rarely) be
of use if the de_table.marked object has already been created,
or if reciprocal tests are not wanted.
A table of automagically-generated labels for each query group, given their similarity to reference groups.
The columns in this table:
test_group : Query group e.g. "c1"
shortlab : The cluster label described above e.g. "c1:macrophage"
pval : If there is a similarity flagged, this is the P-value from a Mann-Whitney U test from the last 'matched' group to the adjacent 'non-matched' group. Ie. If only one label in shortlab, this will be the first of the stepped_pvals, if there are 2, it will be the second. If there is 'no_similarity' this will be NA (Because there is no confidence in what is the most appropriate of the all non-significant stepped pvalues.).
stepped_pvals : P-values from Mann-Whitney U tests across adjacent pairs of reference groups ordered from most to least similar (ascending median rank). ie. 1st-2nd most similar first, 2nd-3rd, 3rd-4th e.t.c. The last value will always be NA (no more reference group). e.g. refA:8.44e-10,refB:2.37e-06,refC:0.000818,refD:0.435,refE:0.245,refF:NA
pval_to_random : P-value of test of median rank (of last matched reference group) < random, from binomial test on top gene ranks (being < 0.5).
matches : List of all reference groups that 'match', as described, except it also includes (rare) examples where pval_to_random is not significant. "|" delimited.
reciprocal_matches : List of all reference groups that flagged test group as a match when directon of comparison is reversed. (significant pval and pval_to_random). "|" delimited.
similar_non_match: This column lists any reference groups outside of shortlab that are not signifcantly different to a reported match group. Limited by num_steps, and will never find anything if num_steps==1. "|" delimited. Usually NA.
similar_non_match_detail : P-values for any details about similar_non_match results. These p-values will always be non-significant. E.g. "A > C (p=0.0214,n.s)". "|" delimited. Usually NA.
differences_within : This feild lists any pairs of reference groups in shortlab that are significantly different. "|" delimited. Usually NA.
make_ref_similarity_names_using_marked: Construct some sensible cluster
labels, but using a premade marked table.
contrast_each_group_to_the_rest For
preparing de_table input
get_the_up_genes_for_all_possible_groups
To prepare the de_table.ref.marked input.
# Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") make_ref_similarity_names(de_table.demo_query, de_table.demo_ref) make_ref_similarity_names(de_table.demo_query, de_table.demo_ref, num_steps=3) make_ref_similarity_names(de_table.demo_query, de_table.demo_ref, num_steps=NA) # Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.demo_query, de_table.demo_ref) de_table.marked.reiprocal <- get_the_up_genes_for_all_possible_groups( de_table.demo_ref, de_table.demo_query) make_ref_similarity_names_using_marked(de_table.marked.query_vs_ref, de_table.marked.reiprocal) make_ref_similarity_names_using_marked(de_table.marked.query_vs_ref)# Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") make_ref_similarity_names(de_table.demo_query, de_table.demo_ref) make_ref_similarity_names(de_table.demo_query, de_table.demo_ref, num_steps=3) make_ref_similarity_names(de_table.demo_query, de_table.demo_ref, num_steps=NA) # Make input # de_table.demo_query <- contrast_each_group_to_the_rest(demo_query_se, "demo_query") # de_table.demo_ref <- contrast_each_group_to_the_rest(demo_ref_se, "demo_ref") de_table.marked.query_vs_ref <- get_the_up_genes_for_all_possible_groups( de_table.demo_query, de_table.demo_ref) de_table.marked.reiprocal <- get_the_up_genes_for_all_possible_groups( de_table.demo_ref, de_table.demo_query) make_ref_similarity_names_using_marked(de_table.marked.query_vs_ref, de_table.marked.reiprocal) make_ref_similarity_names_using_marked(de_table.marked.query_vs_ref)
Internal function, called by make_ref_similarity_names_using_marked for each group.
make_ref_similarity_names_for_group(the_test_group, mwtest_res_table, de_table.ref.marked, reciprocal_matches = NA, the_test_dataset, the_ref_dataset, the_pval)make_ref_similarity_names_for_group(the_test_group, mwtest_res_table, de_table.ref.marked, reciprocal_matches = NA, the_test_dataset, the_ref_dataset, the_pval)
the_test_group |
Query group to make name for |
mwtest_res_table |
Mann-whitney test results as constructed
in |
de_table.ref.marked |
The output of
|
reciprocal_matches |
Simplified table of reciprocal matches prepared
within |
the_test_dataset |
A short meaningful name for the experiment. (Should match test_dataset column in de_table.marked) |
the_ref_dataset |
A short meaningful name for the experiment. (Should match dataset column in de_table.marked) |
the_pval |
pval as per
|
A tibble with just one group's labelling information, as per
make_ref_similarity_names_using_marked
make_ref_similarity_names_using_marked
Only place that uses this function, details there.
Internal function to compare the distribution of a query datasets 'top' genes between two different reference datasete groups with a Mann–Whitney U test. One directional test if groupA median < group B.
run_pair_test_stats(de_table.ref.marked, the_test_group, groupA, groupB, enforceAgtB = TRUE)run_pair_test_stats(de_table.ref.marked, the_test_group, groupA, groupB, enforceAgtB = TRUE)
de_table.ref.marked |
The output of
|
the_test_group |
Name of the test group in query dataset. |
groupA |
One of the reference group names |
groupB |
Another of the reference group names |
enforceAgtB |
Do a one tailed test of A 'less' B (more similar)? Or two-tailed. Default = TRUE. |
For use by make_ref_similarity_names_using_marked
A tibble of wilcox / man-whitneyU test results for this contrast.
make_ref_similarity_names_using_marked
Utility function to randomly subset very large datasets (that use too much memory). Specify a maximum number of cells to keep per group and use the subsetted version to analysis.
subset_cells_by_group(dataset_se, n.group = 1000)subset_cells_by_group(dataset_se, n.group = 1000)
dataset_se |
Summarised experiment object containing count data. Also requires 'ID' and 'group' to be set within the cell information. |
n.group |
How many cells to keep for each group. Default = 1000 |
The resulting differential expression table de_table will have reduced statistical power. But as long as enough cells are left to reasonably accurately calculate differnetial expression between groups this should be enough for celaref to work with.
Also, this function will lose proportionality of groups (there'll be n.groups or less of each). Consider using the n.group/n.other parameters in contrast_each_group_to_the_rest or contrast_the_group_to_the_rest - which subsets non-group cells independantly for each group. That may be more approriate for tissue type samples which would have similar compositions of cells.
So this function is intended for use when either; the proportionality isn't relevant (e.g. FACs purified cell populations), or, the data is just too big to work with otherwise.
Cells are randomly sampled, so set the random seed (with set.seed()) for consistant results across runs.
dataset_se A hopefully more managably subsetted version of the inputted dataset_se.
contrast_each_group_to_the_rest For alternative method
of subsetting cells proportionally.
dataset_se.30pergroup <- subset_cells_by_group(demo_query_se, n.group=30)dataset_se.30pergroup <- subset_cells_by_group(demo_query_se, n.group=30)
This function for use by contrast_each_group_to_the_rest
downsamples cells from a summarizedExperiment
(dataset_se) - keeping n.group (or all if fewer)
cells from the specified group, and n.other from the rest.
This maintains the proportions of cells in the 'other' part of the
differential expression comparisons.
subset_se_cells_for_group_test(dataset_se, the_group, n.group = Inf, n.other = n.group * 5)subset_se_cells_for_group_test(dataset_se, the_group, n.group = Inf, n.other = n.group * 5)
dataset_se |
Summarised experiment object containing count data. Also requires 'ID' and 'group' to be set within the cell information. |
the_group |
The group being subsetted for |
n.group |
How many cells to keep for each group. Default = Inf |
n.other |
How many cells to keep from everything not in the group. Default = n.group * 5 |
Cells are randomly sampled, so set the random seed (with set.seed()) for consistant results across runs.
dataset_se A hopefully more managably subsetted version of the inputted dataset_se
Calling function contrast_each_group_to_the_rest
subset_cells_by_group Exported function for
subsetting each group independantly upfront.
(For when this approach is still unmanageable)
Filter and return a SummarizedExperiment object (dataset_se) by several metrics:
Cells with at least min_lib_size total reads.
Genes expressed in at least min_detected_by_min_samples cells, at a threshold of min_reads_in_sample per cell.
Remove entire groups (clusters) of cells where there are fewer than min_group_membership cells in that group.
trim_small_groups_and_low_expression_genes(dataset_se, min_lib_size = 1000, min_group_membership = 5, min_reads_in_sample = 1, min_detected_by_min_samples = 5)trim_small_groups_and_low_expression_genes(dataset_se, min_lib_size = 1000, min_group_membership = 5, min_reads_in_sample = 1, min_detected_by_min_samples = 5)
dataset_se |
Summarised experiment object containing count data. Also
requires 'ID' and 'group' to be set within the cell information
(see |
min_lib_size |
Minimum library size. Cells with fewer than this many reads removed. Default = 1000 |
min_group_membership |
Throw out groups/clusters with fewer than this many cells. May change with experiment size. Default = 5 |
min_reads_in_sample |
Require this many reads to consider a gene detected in a sample. Default = 1 |
min_detected_by_min_samples |
Keep genes detected in this many samples. May change with experiment size. Default = 5 |
If it hasn't been done already, it is highly reccomended to use this function to filter out genes with no/low total counts (especially in single cell data, there can be many) - without expression they are not useful and may reduce statistical power.
Likewise, very small groups (<5 cells) are unlikely to give useful results with this method. And cells with abnormally small library sizes may not be desireable.
Of course 'reasonable' thresholds for filtering cells/genes are subjective. Defaults are moderately sensible starting points.
A filtered dataset_se, ready for use.
demo_query_se.trimmed <- trim_small_groups_and_low_expression_genes(demo_query_se) demo_query_se.trimmed2 <- trim_small_groups_and_low_expression_genes(demo_ref_se, min_group_membership = 10)demo_query_se.trimmed <- trim_small_groups_and_low_expression_genes(demo_query_se) demo_query_se.trimmed2 <- trim_small_groups_and_low_expression_genes(demo_ref_se, min_group_membership = 10)