default_af_transform(), transformation failed
if NAs were present in the columnsmagrittrdata.table now it’s completely
optional and will be used internally only if the package is availableImports to Suggests - functions
will notify when additional packages are requested for the specific
functionalityavailable_tags()HSC_population_size_estimate() now better supports the
computation of estimates from different groups of cell types and
tissues at the same time. The tabular output now contains an
additional column “Timepoints_included” that specifies how many time
points the estimate containsis_sharing() can now handle better limit cases and has the
option of being parallelised provided appropriate packages are
available (better performance)import_parallel_Vispa2Matrices_auto() and
import_parallel_Vispa2Matrices_interactive() are officially defunct
and will not be exported anymore starting from the next release cyclemode of import_parallel_Vispa2Matrices() no longer
accepts INTERACTIVE as a valid option and the interactive mode is
considered now defunct, since the usage is very limiting and limitedassociation_file of import_parallel_Vispa2Matrices()
no longer accepts a string representing a path. Association file
import is delegated solely to its dedicated function from now on.threshold_filter() is deprecated, since its use is
rather complicated instead of using standard filtering with dplyr or
similar toolsdefault_af_transform() now pads time points based on the maximum
number of characters + 1 in the columntop_abund_tableGrob() - now
the function has a new argument transform_by which is useful for
controlling ordering of columnsDT has been moved (likely temporarily) in Imports - linked
to issue https://github.com/calabrialab/ISAnalytics/issues/2tidyselect warnings (internal use of .data$ in selection
context)gene_frequency_fisherprogressr, added a wrapper function for fast enabling
progress bars, enable_progress_bars()HSC_population_size_estimate() -
signals eventual problems in computing estimates and whyCIS_grubbs function is now faster (removed dependency from
psych::describe)CIS_grubbs_overtime() and associated plotting function
top_cis_overtime_heatmap() to compute CIS_grubbs test over timeimport_association_file() - function had minor
issues when importing *.xlsx files and missing optional columns threw
errorsas_sparse_matrix() - function failed when trying to
process an aggregated matrixexport_ISA_settings() and
import_ISA_settings() that allow a faster workflow setupcompute_near_integrations() - function errored
when report_path argument was set to NULLintegration_alluvial_plot() internalsremove_collisions() use again dplyr internally for
joining and grouping operations - needed because of performance issues
with data.tablefisher_scatterplot() has 2 new arguments that allow the disabling of
highlighting for some genes even if their p-value is under the
thresholdvignette("workflow_start", package="ISAnalytics")gene_frequency_fisher() is a new function of the analysis family
that allows the computation of Fisher’s exact test p-values on gene
frequency - fisher_scatterplot() is the associated plotting functiontop_targeted_genes() is a new function of the analysis family that
produces the top n targeted genes based on the number of ISNGSdataExplorer() is a newly implemented Shiny interface that allows
the exploration and plotting of datagenerate_default_folder_structure()
generates the standard folder structure with package-included data
on-demandtransform_columns() is a new utility function, also used internally
by other exported functions, that allows arbitrary transformations on
data frame columnsremove_collisions() now has a dedicated parameter to specify how
independent samples are identifiedcompute_near_integration_sites() now has a parameter called
additional_agg_lambda() to allow aggregation of additional columnsCIS_grubbs() now signals if there are missing genes in the refgenes
table and eventually returns them as a dfoutlier_filter() is now able to take multiple tests in input and
combine them with a given logic. It now also produces an HTML report.integration_alluvial_plot()import_Vispa2_stats() - function failed when
passing report_path = NULLcircos_genomic_density() when trying to use a
pdf deviceunzip_file_system() was made defunct in favor of
generate_default_folder_structure()cumulative_count_union() was deprecated and its functionality was
moved to cumulative_is()fragmentEstimate_column and
fragmentEstimate_threshold in HSC_population_size_estimate().
Slightly revised filtering logic.max_workers in function remove_collisions()aggregate_metadata()import_Vispa2_stats() from
import_association_file()remove_collisions(): if process
fails function doesn’t stopiss_source()refGenes_mm9 and function
compute_near_integrations()purity_filter()is_sharing() function, detailed usage in vignette
vignette("sharing_analyses", package = "ISAnalytics")cumulative_is()sharing_venn()vignette("report_system", package = "ISAnalytics")ISAnalytics.widgets option has been replaced by
ISAnalytics.reportsremove_collisions(), removed arguments seq_count_col,
max_rows_reports and save_widget_path, added arguments
quant_cols and report_path (see documentation for details)import_single_Vispa2Matrix() now allows keeping additional
non-standard columnscompute_near_integrations() is now faster on bigger data setscolumns and key in
compute_abundance()compute_near_integrations() now produces only re-calibration map in
*.tsv formatCIS_grubbs() now supports calculations for each group specified in
argument bysample_statistics() now there is the option to include the
calculation of distinct integration sites for each group (if mandatory
vars are present)circos_genomic_density()import_parallel_Vispa2Matrices_interactive() and
import_parallel_Vispa2Matrices_auto() are officially deprecated in
favor of import_parallel_Vispa2Matrices()is_sharing computes the sharing of IS between groupssharing_heatmap allows visualization of sharing data through
heatmapsintegration_alluvial_plot allows visualization of integration sites
distribution in groups over time.top_abund_tableGrob can be used in combination with the previous
function or by itself to obtain a summary of top abundant integrations
as an R graphic (tableGrob) object that can be combined with plots.default_statsgenerate_Vispa2_launch_AFHSC_population_size_estimate and HSC_population_plot allow
estimates on hematopoietic stem cell population sizeimport_Vispa2_statsoutlier_filter and outliers_by_pool_fragments offer a mean to
filter poorly represented samples based on custom outliers testsimport_stats of aggregate_metadata is officially
deprecated in favor of import_Vispa2_statsaggregate_metadata is now a lot more flexible on what operations can
be performed on columns via the new argument aggregating_functionsimport_association_file allows directly for the import of Vispa2
stats and converts time points to months and years where not already
presentimport_association_file now produces 3
separate columns for pathsseparate_quant_matrices and comparison_matrix now do not require
mandatory columns other than the quantifications - this allows for
separation or joining also for aggregated matricesCIS_volcano_plot that caused duplication of
some labels if highlighted genes were provided in inputcompute_near_integrations: when provided
recalibration map export path as a folder now the function works
correctly and produces an automatically generated file nameaggregate_metadata: now paths to folder that contains
Vispa2 stats is looked up correctly. Also, VISPA2 stats columns are
aggregated if found in the input data frame independently from the
parameter import_stats.compute_abundance can now take as input aggregated matrices and has
additional parameters to offer more flexibility to the user. Major
updates and improvements also on documentation and reproducible
examples.import_single_Vispa2Matrix: import is
now preferentially carried out using data.table::fread greatly
speeding up the process - where not possible readr::read_delim is
used insteadimport_association_file: greatly
improved parsing precision (each column has a dedicated type), import
report now signals parsing problems and their location and signals
also problems in parsing dates. Report also includes potential
problems in column names and signals missing data in important
columns. Added also the possibility to give various file formats in
input including *.xls(x) formats.top_integrations can now take additional parameters to
compute top n genes for each specified groupCIS_volcano_plot due to poor
precision (easier to add faceting manually) and added parameters to
return the data frame that generated the plot as an additional result.
Also, it is now possible to specify a vector of gene names to
highlight even if they’re not above the annotation threshold.remove_collisionsCIS_grubbs and cumulative_count_unionCIS_volcano_plotsample_statisticsaggregate_values_by_key has a simplified interface and supports
multi-quantification matricesimport_parallel_Vispa2Matrices_interactive and
import_parallel_Vispa2Matrices_auto now have an option to return a
multi-quantification matrix directly after import instead of a listthreshold_filter, top_integrationscompute_abundancecomparison_matrix that ignored custom column namesISanalytics is officially on bioconductor!
comparison_matrix and
separate_quant_matricesas_sparse_matrixcompute_near_integrationsremove_collisionsimport_single_Vispa2Matrix to remove non significant 0
valuesISADataFrame: now the package only uses standard
tibbles