Package 'TMSig' reference manual

Title:	Tools for Molecular Signatures
Description:	The TMSig package contains tools to prepare, analyze, and visualize named lists of sets, with an emphasis on molecular signatures (such as gene or kinase sets). It includes fast, memory efficient functions to construct sparse incidence and similarity matrices and filter, cluster, invert, and decompose sets. Additionally, bubble heatmaps can be created to visualize the results of any differential or molecular signatures analysis.
Authors:	Tyler Sagendorf [aut, cre] , Di Wu [ctb], Gordon Smyth [ctb]
Maintainer:	Tyler Sagendorf <[email protected]>
License:	GPL (>= 3)
Version:	1.1.0
Built:	2024-10-31 06:21:31 UTC
Source:	https://github.com/bioc/TMSig

Competitive Gene Set Test Accounting for Inter-gene Correlation

Description

Pre-ranked Correlation-Adjusted MEan RAnk gene set testing (CAMERA-PR) tests whether a set of genes is highly ranked relative to other genes in terms of some measure of differential expression, accounting for inter-gene correlation (Wu & Smyth, 2012). See cameraPR for details.

While the language is gene-centric, any a priori groups of molecules may be tested.

Usage

## S3 method for class 'matrix'
cameraPR(
  statistic,
  index,
  use.ranks = FALSE,
  inter.gene.cor = 0.01,
  sort = TRUE,
  alternative = c("two.sided", "less", "greater"),
  adjust.globally = FALSE,
  min.size = 2L,
  ...
)
## S3 method for class 'matrix'
cameraPR(
  statistic,
  index,
  use.ranks = FALSE,
  inter.gene.cor = 0.01,
  sort = TRUE,
  alternative = c("two.sided", "less", "greater"),
  adjust.globally = FALSE,
  min.size = 2L,
  ...
)

Arguments

`statistic`	a matrix of statistics (moderated z-statistics preferred) with genes/molecules as row names and one or more contrasts or coefficients as column names. Missing values are allowed.
`index`	a named list of sets to test. Passed to `sparseIncidence`. `index` must be a list of character vectors, not the result of `ids2indices`, so it is more restrictive than what `cameraPR.default` allows.
`use.ranks`	logical; whether to perform a parametric test (`FALSE`; default) or a rank-based test (`TRUE`).
`inter.gene.cor`	numeric; the inter-gene correlation within tested sets. May be a single value or a named vector with names matching those of `index`.
`sort`	logical; should the results of each contrast be sorted by p-value? Default is `TRUE`.
`alternative`	character; the alternative hypothesis. Must be one of "`two.sided`" (default), "`greater`", or "`less`". May be abbreviated.
`adjust.globally`	logical; whether p-values from different contrasts should be adjusted together. It is recommended to set this to `TRUE` when testing a set of closely related contrasts. See Section 13.3 of the LIMMA User's Guide (`limmaUsersGuide`) for details. Default is `FALSE`.
`min.size`	integer; the minimum set size. To be considered for testing, sets must have at least `min.size` elements with non-missing values in all contrasts. The default value of 2 is the minimum possible set size required for testing, though a value of 10 or higher is recommended; higher values tend to produce more robust results.
`...`	other arguments are not currently used

Value

A data.frame with the following columns:

`Contrast`	factor; the contrast of interest.
`GeneSet`	character; the gene set being tested.
`NGenes`	integer; number of genes in the set with values in the `statistic` matrix for a given contrast.
`Correlation`	numeric; inter-gene correlation (only included if `inter.gene.cor` was not a single value).
`Direction`	character; direction of change ("Up" or "Down").
`TwoSampleT`	numeric; two-sample t-statistic (only included if `use.ranks=FALSE`).
`df`	integer; degrees of freedom (only included if `use.ranks=FALSE`). Two less than the number of non-missing values in each column of the `statistic` matrix.
`ZScore`	numeric; the z-score equivalent of `TwoSampleT`.
`PValue`	numeric; one- or two-sided (if `alternative="two.sided"`) p-value.
`FDR`	numeric; Benjamini and Hochberg FDR adjusted p-value.

Test Assumptions

If use.ranks=FALSE, the parametric version of CAMERA-PR will be used. Since this is a modification of Student's two sample t-test, it is assumed that the statistics in each column of statistic are approximately Normally distributed. In camera.default, the moderated t-statistics are converted to z-statistics with zscoreT and used for the analysis.

If use.ranks=TRUE, a modified Wilcoxon-Mann-Whitney rank sum test will be used.

Author(s)

CAMERA-PR was developed by Di Wu and Gordon Smyth (2012). With permission, Tyler Sagendorf modified their original code to create the matrix method. If using cameraPR.matrix, please cite the original paper, as well as the TMSig R package.

References

Wu, D., and Smyth, G. K. (2012). Camera: a competitive gene set test accounting for inter-gene correlation. Nucleic Acids Research 40, e133. doi:10.1093/nar/gks461.

Goeman, J. J., and Bühlmann, P. (2007). Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics 23, 980-987. doi:10.1093/bioinformatics/btm051.

Examples

require(stats)

# Simulate experimental data with control and treatment groups (3 samples
# each)
group <- rep(c("control", "treatment"), each = 3)
design <- model.matrix(~ 0 + group)
contrasts <- makeContrasts(contrasts = "grouptreatment - groupcontrol",
                           levels = colnames(design))

ngenes <- 1000L
nsamples <- length(group)

set.seed(0)
y <- matrix(data = rnorm(ngenes * nsamples),
            nrow = ngenes, ncol = nsamples,
            dimnames = list(paste0("gene", seq_len(ngenes)),
                            make.unique(group)))

# First set of 20 genes are genuinely differentially expressed
# (trt1 and trt2 are lower than control)
index1 <- 1:20
y[index1, 1:3] <- y[index1, 1:3] + 1

# Second set of 20 genes are not DE
index2 <- 21:40

# Generate matrix of moderated t-statistics
fit <- lmFit(y, design)
fit.contr <- contrasts.fit(fit, contrasts = contrasts)
fit.smooth <- eBayes(fit.contr)

index <- list(set1 = rownames(y)[index1],
              set2 = rownames(y)[index2])

# Compute z-score equivalents of moderated t-statistics
statistic <- zscoreT(fit.smooth$t, fit.smooth$df.total)
head(statistic)

# Only set1 is DE
cameraPR(statistic = statistic, index = index)

# Non-parametric version
cameraPR(statistic = statistic, index = index, use.ranks = TRUE)
require(stats)

# Simulate experimental data with control and treatment groups (3 samples
# each)
group <- rep(c("control", "treatment"), each = 3)
design <- model.matrix(~ 0 + group)
contrasts <- makeContrasts(contrasts = "grouptreatment - groupcontrol",
                           levels = colnames(design))

ngenes <- 1000L
nsamples <- length(group)

set.seed(0)
y <- matrix(data = rnorm(ngenes * nsamples),
            nrow = ngenes, ncol = nsamples,
            dimnames = list(paste0("gene", seq_len(ngenes)),
                            make.unique(group)))

# First set of 20 genes are genuinely differentially expressed
# (trt1 and trt2 are lower than control)
index1 <- 1:20
y[index1, 1:3] <- y[index1, 1:3] + 1

# Second set of 20 genes are not DE
index2 <- 21:40

# Generate matrix of moderated t-statistics
fit <- lmFit(y, design)
fit.contr <- contrasts.fit(fit, contrasts = contrasts)
fit.smooth <- eBayes(fit.contr)

index <- list(set1 = rownames(y)[index1],
              set2 = rownames(y)[index2])

# Compute z-score equivalents of moderated t-statistics
statistic <- zscoreT(fit.smooth$t, fit.smooth$df.total)
head(statistic)

# Only set1 is DE
cameraPR(statistic = statistic, index = index)

# Non-parametric version
cameraPR(statistic = statistic, index = index, use.ranks = TRUE)

Similarity-Based Clustering of Sets

Description

Determine clusters of highly similar sets. Used to reduce the redundancy of sets prior to statistical analysis.

Usage

clusterSets(
  x,
  type = c("jaccard", "overlap", "otsuka"),
  cutoff = 0.85,
  method = "complete",
  h = 0.9
)
clusterSets(
  x,
  type = c("jaccard", "overlap", "otsuka"),
  cutoff = 0.85,
  method = "complete",
  h = 0.9
)

Arguments

`x`	a named list of sets. Elements must be of type `"character"`.
`type`	character; the type of similarity measure to use. Either `"jaccard"`, `"overlap"`, or `"otsuka"`. May be abbreviated.
`cutoff`	numeric 0-1; minimum similarity coefficient required to classify two sets as being similar. Default is 0.85.
`method`	character; the clustering method passed to `hclust`. Default is "complete", so sets will only be included in a cluster if their similarity to all other sets in that cluster is $\geq$ `cutoff`.
`h`	numeric 0-1; cut height used to define clusters. Passed to `cutree`. Default is 0.9.

Value

A data.frame with 3 columns:

`set`	character; the name of the set.
`cluster`	integer; the cluster identifier.
`set_size`	integer; the size of the set (number of elements).

Results are arranged in ascending order by cluster, descending order by set size, and then alphanumerically by set name.

Function Details

Given a named list of sets, clusterSets calculates all pairwise Jaccard, overlap, or Ōtsuka similarity coefficients (see similarity for details). Any coefficients below cutoff are set to 0 and complete-linkage hierarchical clustering is performed on the dissimilarity matrix (calculated as 1 - coefficients). Lastly, cutree is used with cut height h to define clusters, and the results are stored in a data.frame.

Optimization

Clustering does not need to be performed on those sets that are not sufficiently similar (value of similarity below cutoff) to any other set, as they will always be placed in their own cluster. By excluding these sets during the hierarchical clustering step, the speed of clusterSets will increase as the value of cutoff approaches 1 (as the size of the dissimilarity matrix decreases).

Minimum Set Size

Sets that are not sufficiently large will always appear as singleton clusters, unless they are aliased or subsets (overlap similarity only). For two sets $A$ and $B$ to be sufficiently similar, defined as having a similarity coefficient at least equal to some cutoff (e.g., $Jaccard~\geq~x$ ), they must have minimum sizes $|A|$ , $|B|$ , and intersection size $|A \cap B|$ :

Jaccard: $|A| = \lceil \frac{x}{1 - x} \rceil, \quad |B| = 1 + |A|, \quad |A \cap B| = |A|$
Overlap: $|A| = |B| = 1 + \lceil \frac{x}{1 - x} \rceil, \quad |A \cap B| = |A| - 1$
Ōtsuka: $|A| = \lceil \frac{x^2}{1 - x^2} \rceil, \quad |B| = 1 + |A|, \quad |A \cap B| = |A|$

where $\lceil y \rceil$ is the ceiling function applied to some real number $y$ .

For example, if the cutoff is $x = 0.85$ , then the minimum set and intersection sizes are

Jaccard: $|A| = 6, \quad |B| = 7, \quad |A \cap B| = 6$
Overlap: $|A| = |B| = 7, \quad |A \cap B| = 6$
Ōtsuka: $|A| = 3, \quad |B| = 4, \quad |A \cap B| = 3$

That is, sets with fewer elements or smaller intersections will always appear as singleton clusters unless they are aliased or, in the case of the overlap similarity, subsets.

Source

This function is based on the procedure described in the Molecular Signatures Database (MSigDB) v7.0 Release Notes (Liberzon 2011, 2015): https://docs.gsea-msigdb.org/#MSigDB/Release_Notes/MSigDB_7.0/. Specifically, sections "C2:CP:Reactome — Major Overhaul" and "C5 (Gene Ontology Collection) — Major Overhaul". Though hierarchical clustering is widely used, the defaults are exactly what is set for MSigDB (private correspondence).

References

Liberzon, A., Subramanian, A., Pinchback, R., Thorvaldsdóttir, H., Tamayo, P., & Mesirov, J. P. (2011). Molecular signatures database (MSigDB) 3.0. Bioinformatics, 27(12), 1739–1740. doi:10.1093/bioinformatics/btr260

Liberzon, A., Birger, C., Thorvaldsdóttir, H., Ghandi, M., Mesirov, J. P., & Tamayo, P. (2015). The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell systems, 1(6), 417–425. doi:10.1016/j.cels.2015.12.004

Examples

x <- list("A" = letters[1:5],
          "B" = letters[1:4], # subset of A
          "C" = letters[1:4], # aliased with B
          "D" = letters[1:3], # subset of A, B, C
          "E" = c("a", "a", NA), # duplicates and NA
          "F" = c("x", "y", "z"), # distinct elements
          "G" = letters[3:6]) # overlaps with A-E

# Default clustering based on Jaccard similarity
clusterSets(x)
clusterSets(x, type = "overlap") # overlap similarity
clusterSets(x, type = "otsuka") # Ōtsuka similarity

# Relax Jaccard similarity cutoff
(df <- clusterSets(x, cutoff = 0.5))

# Keep the first (largest) set from each cluster
with(df, set[!duplicated(cluster)]) # A, G, E, F

# Keep the smallest set from each cluster
df <- df[order(df$set_size), ]
with(df, set[!duplicated(cluster)]) # E, D, F, G

# Cluster aliased sets (type = "otsuka" would produce
# identical results)
clusterSets(x, type = "jaccard", cutoff = 1)

# Cluster subsets and aliased sets
clusterSets(x, type = "overlap", cutoff = 1)
x <- list("A" = letters[1:5],
          "B" = letters[1:4], # subset of A
          "C" = letters[1:4], # aliased with B
          "D" = letters[1:3], # subset of A, B, C
          "E" = c("a", "a", NA), # duplicates and NA
          "F" = c("x", "y", "z"), # distinct elements
          "G" = letters[3:6]) # overlaps with A-E

# Default clustering based on Jaccard similarity
clusterSets(x)
clusterSets(x, type = "overlap") # overlap similarity
clusterSets(x, type = "otsuka") # Ōtsuka similarity

# Relax Jaccard similarity cutoff
(df <- clusterSets(x, cutoff = 0.5))

# Keep the first (largest) set from each cluster
with(df, set[!duplicated(cluster)]) # A, G, E, F

# Keep the smallest set from each cluster
df <- df[order(df$set_size), ]
with(df, set[!duplicated(cluster)]) # E, D, F, G

# Cluster aliased sets (type = "otsuka" would produce
# identical results)
clusterSets(x, type = "jaccard", cutoff = 1)

# Cluster subsets and aliased sets
clusterSets(x, type = "overlap", cutoff = 1)

Decompose Pairs of Overlapping Sets Into 3 Disjoint Parts

Description

Decompose all pairs of sufficiently overlapping sets into 3 disjoint parts: the elements unique to the first set, the elements unique to the second set, and the elements found in both sets. See the examples section in invertSets for a method to decompose an entire list of sets.

Usage

decomposeSets(
  x,
  overlap = 1L,
  AND = "~AND~",
  MINUS = "~MINUS~",
  verbose = TRUE
)
decomposeSets(
  x,
  overlap = 1L,
  AND = "~AND~",
  MINUS = "~MINUS~",
  verbose = TRUE
)

Arguments

`x`	a named list of sets. Elements must be of type `"character"`.
`overlap`	integer; only pairs of sets with at least `overlap` elements in common will be decomposed.
`AND`	character; string used to denote the intersection of two sets. Defaut is "~AND~", which produces intersections of the form "A ~AND~ B" (i.e., elements in both A and B).
`MINUS`	character; string used to denote the difference of two sets. Defualt is "~MINUS~", which produces differences of the form "A ~MINUS~ B" (i.e., elements in A and not in B).
`verbose`	logical; whether to print warnings and messages.

Value

A named list of disjoint parts of sets. May contain aliases.

Optimization

Since the size of the intersection between two sets is at most the size of the smaller set, any sets with fewer than overlap elements can be immediately discarded.

Source

Decomposition of sets is described by Jiang and Gentleman (2007) in section 2.3.1 "Overlap among gene sets". It is a method to reduce the redundancy of significant gene set testing results whereby the decomposed sets are reanalyzed and the following selections can be made:

If the elements unique to set 1 and set 2, elements common to both sets, or all 3 parts are statistically significant, keep both set 1 and set 2 in the original results. We can not separate their effects.
If the elements unique to set 1 or the elements unique to set 1 and common to both sets are statistically significant, only keep set 1 in the original results. (The same logic can be applied for set 2.)

References

Jiang, Z., & Gentleman, R. (2007). Extensions to gene set enrichment. Bioinformatics, 23(3), 306–313. doi:10.1093/bioinformatics/btl599

Examples

x <- list("A" = letters[1:10],
          "B" = letters[3:7],
          "C" = letters[1:4],
          "D" = letters[6:12])

decomposeSets(x)

decomposeSets(x, overlap = 5L)
x <- list("A" = letters[1:10],
          "B" = letters[3:7],
          "C" = letters[1:4],
          "D" = letters[6:12])

decomposeSets(x)

decomposeSets(x, overlap = 5L)

Set Enrichment Bubble Heatmap

Description

Create a bubble heatmap summarizing molecular signature analysis results, such as those from cameraPR.matrix. May also be used to generate bubble heatmaps of differential analysis results.

Usage

enrichmap(
  x,
  n_top = 15L,
  set_column = "GeneSet",
  statistic_column = "ZScore",
  contrast_column = "Contrast",
  padj_column = "FDR",
  padj_legend_title = padj_column,
  padj_aggregate_fun = function(padj) median(-log10(padj), na.rm = TRUE),
  padj_cutoff = 0.05,
  plot_sig_only = TRUE,
  padj_fill = "grey",
  colors = c("#3366ff", "darkred"),
  heatmap_color_fun = cameraColorFun,
  scale_by = c("row", "column", "max"),
  cell_size = unit(14, "points"),
  filename,
  height = 5,
  width = 5,
  units = "in",
  heatmap_args = list(),
  padj_args = list(),
  save_args = list(),
  draw_args = list()
)
enrichmap(
  x,
  n_top = 15L,
  set_column = "GeneSet",
  statistic_column = "ZScore",
  contrast_column = "Contrast",
  padj_column = "FDR",
  padj_legend_title = padj_column,
  padj_aggregate_fun = function(padj) median(-log10(padj), na.rm = TRUE),
  padj_cutoff = 0.05,
  plot_sig_only = TRUE,
  padj_fill = "grey",
  colors = c("#3366ff", "darkred"),
  heatmap_color_fun = cameraColorFun,
  scale_by = c("row", "column", "max"),
  cell_size = unit(14, "points"),
  filename,
  height = 5,
  width = 5,
  units = "in",
  heatmap_args = list(),
  padj_args = list(),
  save_args = list(),
  draw_args = list()
)

Arguments

`x`	an object that can be coerced to a `data.table` with columns `contrast_column`, `set_column`, `statistic_column`, and `padj_column`.
`n_top`	integer; number of sets (rows) to display. Defaults to the top 15 sets with the highest median $-log_{10}$ (adjusted p-values) across contrasts.
`set_column`	character; the name of a column in `x` containing unique set identifiers that will be used as the row names in the heatmap. Default is "GeneSet".
`statistic_column`	character; the name of a column in `x` containing the statistic for each combination of contrast and molecular signature. Determines the heatmap body colors. Default is "ZScore".
`contrast_column`	character; the name of a column in `x` containing contrasts that will be used as columns for the heatmap. Entries of `x[[rownames_colum]]` must be uniquely defined for each contrast group.
`padj_column`	character; the name of a column in `x` containing the adjusted p-values. Determines the diameter of each bubble in the heatmap.
`padj_legend_title`	character; title of the background fill legend. Defaults to `padj_column`.
`padj_aggregate_fun`	function; a function used to aggregate the adjusted p-values in `x[[pvalue_column]]` across contrasts for each unique entry in `x[[set_column]]`. The default computes the median of the $-log_{10}$ adjusted p-values.
`padj_cutoff`	numeric; cutoff for terms to be statistically significant. If `plot_sig_only=TRUE`, only those molecular signatures with at least one `padj_column` value less than this threshold may appear in the heatmap. Default is 0.05.
`plot_sig_only`	logical; whether to plot only those `n_top` terms that have at least one `padj_column` value less than `padj_cutoff`.
`padj_fill`	character; the background color used for values in `padj_column` that are less than `padj_cutoff`. Default is "grey".
`colors`	character; vector of length 2 specifying the colors for the largest negative and largest positive values of `x[[statistic_column]]`, respectively. Default is "#3366ff" (blue) and "darkred".
`heatmap_color_fun`	function; used to create the legend for the heatmap bubble fill. See `enrichmapColorFunctions` for details.
`scale_by`	character; whether to scale the bubbles such that the term with the largest $-log_{10}$ adjusted p-value in each row (`scale_by="row"`), column (`scale_by="column"`), or overall (`scale_by="max"`) is of maximum diameter. Default is "row" to better visualize patterns across contrasts. May be abbreviated.
`cell_size`	`unit` object; the size of each heatmap cell (used for both height and width). Default is `unit(14, "points")`. This also controls the default text size, which defaults to 90% the size of `cell_size`.
`filename`	character; the file name used to save the heatmap. If missing (default), the heatmap will be displayed instead.
`height`	numeric; height of the file in `units`.
`width`	numeric; width of the file in `units`.
`units`	character; units that define `height` and `width`. Defaults to "in" (inches). See `unit` for possible units.
`heatmap_args`	list; additional arguments passed to `Heatmap`.
`padj_args`	list; additional arguments passed to `Legend`. Modifies the adjusted p-value legend.
`save_args`	list; additional arguments passed to the graphics device determined by the `filename` extension. See `png` and `pdf` for options.
`draw_args`	list; additional arguments passed to `draw-HeatmapList-method`.

Details

The diameter of each bubble is determined by the $-log_{10}$ adjusted p-values. By default, the bubbles are scaled such that the contrast with the largest $-log_{10}$ adjusted p-value per row (scale_by="row") has a bubble diameter of 0.95 * cell_size, and all other bubbles in that row are scaled relative to this maximum diameter; this is to better visualize patterns across contrasts. Bubbles can also be scaled so that largest $-log_{10}$ adjusted p-value by column (scale_by="column") or in the entire heatmap (scale_by="max") has the maximum diameter. The bubble diameters will be no smaller than 0.2 * cell_size.

Value

Nothing. Displays heatmap or saves the heatmap to a file (if filename is provided).

Examples

## Simulate results of cameraPR.matrix
set.seed(1)
df <- 5000L
x <- data.frame(
    Contrast = rep(paste("Contrast", 1:3), each = 4),
    GeneSet = rep(paste("GeneSet", 1:4), times = 3),
    TwoSampleT = 5 * rt(n = 12L, df = df)
)

# Calculate z-statistics, two-sided p-values, and BH adjusted p-values
x$ZScore <- limma::zscoreT(x = x$TwoSampleT, df = df)
x$PValue <- 2 * pnorm(abs(x$ZScore), lower.tail = FALSE)
x$FDR <- p.adjust(x$PValue, method = "BH")

## Plot results
# Same as enrichmap(x, statistic_column = "ZScore")
enrichmap(x = x,
          set_column = "GeneSet",
          statistic_column = "ZScore",
          contrast_column = "Contrast",
          padj_column = "FDR",
          padj_cutoff = 0.05)

# Include gene sets with adjusted p-values above padj_cutoff (0.05).
# Also update adjusted p-value legend title.
enrichmap(x = x,
          statistic_column = "ZScore",
          plot_sig_only = FALSE,
          padj_legend_title = "BH Adjusted\nP-Value")
## Simulate results of cameraPR.matrix
set.seed(1)
df <- 5000L
x <- data.frame(
    Contrast = rep(paste("Contrast", 1:3), each = 4),
    GeneSet = rep(paste("GeneSet", 1:4), times = 3),
    TwoSampleT = 5 * rt(n = 12L, df = df)
)

# Calculate z-statistics, two-sided p-values, and BH adjusted p-values
x$ZScore <- limma::zscoreT(x = x$TwoSampleT, df = df)
x$PValue <- 2 * pnorm(abs(x$ZScore), lower.tail = FALSE)
x$FDR <- p.adjust(x$PValue, method = "BH")

## Plot results
# Same as enrichmap(x, statistic_column = "ZScore")
enrichmap(x = x,
          set_column = "GeneSet",
          statistic_column = "ZScore",
          contrast_column = "Contrast",
          padj_column = "FDR",
          padj_cutoff = 0.05)

# Include gene sets with adjusted p-values above padj_cutoff (0.05).
# Also update adjusted p-value legend title.
enrichmap(x = x,
          statistic_column = "ZScore",
          plot_sig_only = FALSE,
          padj_legend_title = "BH Adjusted\nP-Value")

Color Functions for enrichmap

Description

Heatmap color functions for plotting GSEA-like and CAMERA-like results with enrichmap.

Usage

gseaColorFun(statistics, colors = c("#3366ff", "darkred"))

cameraColorFun(statistics, colors = c("#3366ff", "darkred"))
gseaColorFun(statistics, colors = c("#3366ff", "darkred"))

cameraColorFun(statistics, colors = c("#3366ff", "darkred"))

Arguments

`statistics`	numeric matrix or vector of statistics. Missing values are removed. Used to compute limits for the color legend.
`colors`	vector of 2 colors for the most negative and most positive values of `statistics`. Default is "#3366ff" (blue) and "darkred".

Details

For gseaColorFun, the statistics are expected to be normalized enrichment scores (NES). Due to how the NES is formulated, values between -1 and 1 are never significant or otherwise interesting, so they are given a white fill so as to not appear in the heatmap (see examples).

Value

a named list of breaks and colors for the heatmap legend.

Examples

set.seed(0)
x <- rnorm(10, mean = 0, sd = 2)

cameraColorFun(x)
cameraColorFun(x[x >= 0]) # positive only

gseaColorFun(x)
gseaColorFun(x[x >= 0]) # positive only
set.seed(0)
x <- rnorm(10, mean = 0, sd = 2)

cameraColorFun(x)
cameraColorFun(x[x >= 0]) # positive only

gseaColorFun(x)
gseaColorFun(x[x >= 0]) # positive only

Extend the Range of Values Out to the Nearest Digit

Description

Extend the Range of Values Out to the Nearest Digit

Usage

extendRangeNum(x, nearest = 1)
extendRangeNum(x, nearest = 1)

Arguments

`x`	any `numeric` object. Passed to `range`.
`nearest`	numeric; the range of `x` will be extended out to the value specified by `nearest`. Default is 1, which extends the range out to the nearest integer.

Value

A numeric vector of length 2 containing the minimum and maximum values of x after extending them outward to the value provided by nearest.

Examples

set.seed(0)
x <- runif(5, min = -10, max = 10)
range(x) # -4.689827  8.164156

extendRangeNum(x) # -5  9
extendRangeNum(x, nearest = 2) # -6  10
extendRangeNum(x, nearest = 0.1) # -4.7  8.2
set.seed(0)
x <- runif(5, min = -10, max = 10)
range(x) # -4.689827  8.164156

extendRangeNum(x) # -5  9
extendRangeNum(x, nearest = 2) # -6  10
extendRangeNum(x, nearest = 0.1) # -4.7  8.2

Filter a Named List of Sets by Size

Description

Given a named list of sets, filter to those that contain at least min_size and no more than max_size elements. The sets are optionally restricted to elements of background before filtering by size.

Usage

filterSets(x, background = NULL, min_size = 5L, max_size = Inf, ...)

## S4 method for signature 'GeneSet,character,numeric,numeric'
filterSets(x, background = NULL, min_size = 5L, max_size = Inf, ...)

## S4 method for signature 'GeneSetCollection,character,numeric,numeric'
filterSets(x, background = NULL, min_size = 5L, max_size = Inf, ...)
filterSets(x, background = NULL, min_size = 5L, max_size = Inf, ...)

## S4 method for signature 'GeneSet,character,numeric,numeric'
filterSets(x, background = NULL, min_size = 5L, max_size = Inf, ...)

## S4 method for signature 'GeneSetCollection,character,numeric,numeric'
filterSets(x, background = NULL, min_size = 5L, max_size = Inf, ...)

Arguments

`x`	a named list of sets. Elements must be of type `"character"`.
`background`	character; optional character vector. `x` will be filtered to only those elements of `background`.
`min_size`	integer ( $\geq 1$ ); the minimum allowable set size.
`max_size`	integer ( $\geq 1$ ); the maximum allowable set size.
`...`	additional arguments are not currently used.

Value

A named list of sets at most the same size as x.

Examples

x <- list("A" = c("a", "b", "c"),
          "B" = c("a", "a", "d", "e", NA), # duplicates and NA
          "C" = c("f", "g"))

# All sets have at least 2 elements,
# so this just removes duplicates and NA
filterSets(x, min_size = 2L)

# Limit scope of sets before filtering
filterSets(x, min_size = 2L, background = c("a", "c", "e", "z"))
x <- list("A" = c("a", "b", "c"),
          "B" = c("a", "a", "d", "e", NA), # duplicates and NA
          "C" = c("f", "g"))

# All sets have at least 2 elements,
# so this just removes duplicates and NA
filterSets(x, min_size = 2L)

# Limit scope of sets before filtering
filterSets(x, min_size = 2L, background = c("a", "c", "e", "z"))

Convert Incidence Matrix to a Named List of Sets

Description

Converts an incidence matrix to a named list of sets. The inverse of sparseIncidence.

Usage

incidenceToList(incidence)
incidenceToList(incidence)

Arguments

incidence

incidence matrix with set names as rows and elements as columns. For instance, the output of sparseIncidence.

Value

a named list of sets with the same length as nrow(incidence).

Note

Currently, there are no checks to ensure incidence is a valid incidence matrix.

Examples

x <- list("A" = c("a", "b", "c"),
          "B" = c("c", "d"),
          "C" = c("x", "y", "z", "z"), # duplicates
          "D" = c("a", NA)) # missing values

(imat <- sparseIncidence(x)) # incidence matrix

incidenceToList(incidence = imat)
x <- list("A" = c("a", "b", "c"),
          "B" = c("c", "d"),
          "C" = c("x", "y", "z", "z"), # duplicates
          "D" = c("a", NA)) # missing values

(imat <- sparseIncidence(x)) # incidence matrix

incidenceToList(incidence = imat)

Invert a List of Sets, Transposing Sets and Elements

Description

Invert a list of sets so that elements become set names and set names become elements.

Usage

invertSets(x, ...)

## S4 method for signature 'GeneSet'
invertSets(x, ...)

## S4 method for signature 'GeneSetCollection'
invertSets(x, ...)
invertSets(x, ...)

## S4 method for signature 'GeneSet'
invertSets(x, ...)

## S4 method for signature 'GeneSetCollection'
invertSets(x, ...)

Arguments

`x`	a named list of sets. Elements must be of type `"character"`.
`...`	additional arguments are not currently used.

Value

A named list of sets.

Note

This function is essentially a more limited version of purrr::transpose_list.

Examples

x <- list("A" = c("a", "b", "c"),
          "B" = c("c", "d"),
          "C" = c("x", "y", "z"),
          "D" = c("a", "c", "d"))

# Invert sets
(y <- invertSets(x))

# Jaccard similarity of pairs of elements
similarity(y)

# Decompose sets into disjoint parts
yc <- lapply(y, paste, collapse = ", ")
invertSets(yc)
x <- list("A" = c("a", "b", "c"),
          "B" = c("c", "d"),
          "C" = c("x", "y", "z"),
          "D" = c("a", "c", "d"))

# Invert sets
(y <- invertSets(x))

# Jaccard similarity of pairs of elements
similarity(y)

# Decompose sets into disjoint parts
yc <- lapply(y, paste, collapse = ", ")
invertSets(yc)

Read GMT File to a Named List of Sets

Description

Create a named list of sets from a GMT file, or a file structured like a GMT.

Usage

readGMT(path, check = TRUE)
readGMT(path, check = TRUE)

Arguments

`path`	character; path to a GMT file. Files may include one additional extension after ".gmt", such as ".gmt.gzip".
`check`	logical; check that `path` points to a valid GMT file. If `FALSE`, files with different extensions may be read, so long as they are in the expected format.

Details

The second entry in each line of the GMT file is assumed to be a URL or some other additional information, so it is discarded.

Value

A named list of character vectors.

Note

Similar to fgsea::gmtPathways.

Examples

path <- system.file("extdata", "c5.go.v2023.2.Hs.symbols.gmt.gz",
                    package = "TMSig")

x <- readGMT(path)

head(names(x)) # First 6 gene set names

x[1] # first set
path <- system.file("extdata", "c5.go.v2023.2.Hs.symbols.gmt.gz",
                    package = "TMSig")

x <- readGMT(path)

head(names(x)) # First 6 gene set names

x[1] # first set

Construct a Matrix of Pairwise Set Similarity Coefficients

Description

Construct a sparse matrix of similarity coefficients for each pair of sets in a list.

Usage

similarity(x, type = c("jaccard", "overlap", "otsuka"))
similarity(x, type = c("jaccard", "overlap", "otsuka"))

Arguments

`x`	a named list of sets. Elements must be of type `"character"`.
`type`	character; the type of similarity measure to use. Either `"jaccard"`, `"overlap"`, or `"otsuka"`. May be abbreviated.

Value

A symmetric dgCMatrix containing all pairwise set similarity coefficients.

Set Similarity

If $A$ and $B$ are sets, we define the Jaccard similarity coefficient $J$ as the size of their intersection divided by the size of their union (Jaccard, 1912):

$\text{J}(A, B) = \frac{|A \cap B|}{|A \cup B|}$

The overlap coefficient is defined as the size of the intersection divided by the size of the smaller set (Simpson, 1943, 1947, 1960; Fallaw 1979):

$\text{Overlap}(A, B) = \frac{|A \cap B|}{min(|A|, |B|)}$

The Ōtsuka coefficient is defined as the size of the intersection divided by the geometric mean of the set sizes (Ōtsuka, 1936), which is equivalent to the cosine similarity of two bit vectors:

$\text{Ōtsuka}(A, B) = \frac{|A \cap B|}{\sqrt{|A| \times |B|}}$

The Jaccard and Ōtsuka coefficients can identify aliased sets (sets which contain the same elements, but have different names), while the overlap coefficient can identify both aliased sets and subsets. Aliases and subsets are not easily distinguished without also having the matrix of Jaccard (or Ōtsuka) coefficients or the set sizes.

Notice the relationship between the similarity coefficients:

$0 \leq \text{J}(A, B) \leq \text{Ōtsuka}(A, B) \leq \text{Overlap}(A, B) \leq 1$

Optimization

Calculations are only performed for pairs of sets with nonzero intersections in the lower triangular part of the matrix. As such, similarity is efficient even for large similarity matrices, and it is especially efficient for sparse similarity matrices.

References

Jaccard, P. (1912). The distribution of the flora in the alpine zone. The New Phytologist, 11(2), 37–50. doi:10.1111/j.1469-8137.1912.tb05611.x. https://www.jstor.org/stable/2427226

Ōtsuka, Y. (1936). The faunal character of the Japanese Pleistocene marine Mollusca, as evidence of the climate having become colder during the Pleistocene in Japan. Bulletin of the Biogeographical Society of Japan, 6(16), 165–170.

Simpson, G. G. (1943). Mammals and the nature of continents. American Journal of Science, 241(1), 1–31.

Simpson, G. G. (1947). Holarctic mammalian faunas and continental relationships during the Cenozoic. Bulletin of the Geological Society of America, 58(7), 613–688.

Simpson, G. G. (1960). Notes on the measurement of faunal resemblance. American Journal of Science, 258-A, 300–311.

Fallaw, W. C. (1979). A test of the Simpson coefficient and other binary coefficients of faunal similarity. Journal of Paleontology, 53(4), 1029–1034. http://www.jstor.org/stable/1304126

Examples

x <- list("A" = c("a", "b", "c", "d", "e"),
          "B" = c("d", "e", "f", "g"), # overlaps with A
          "C" = c("d", "e", "f", "g"), # aliased with B
          "D" = c("a", "b", "c")) # subset of A

similarity(x) # Jaccard coefficients

similarity(x, type = "overlap") # overlap coefficients

similarity(x, type = "otsuka") # Ōtsuka coefficients
x <- list("A" = c("a", "b", "c", "d", "e"),
          "B" = c("d", "e", "f", "g"), # overlaps with A
          "C" = c("d", "e", "f", "g"), # aliased with B
          "D" = c("a", "b", "c")) # subset of A

similarity(x) # Jaccard coefficients

similarity(x, type = "overlap") # overlap coefficients

similarity(x, type = "otsuka") # Ōtsuka coefficients

Construct a Sparse Incidence Matrix

Description

Construct a sparse incidence matrix from a named list of sets.

Usage

sparseIncidence(x, ...)

## S4 method for signature 'GeneSet'
sparseIncidence(x, ...)

## S4 method for signature 'GeneSetCollection'
sparseIncidence(x, ...)
sparseIncidence(x, ...)

## S4 method for signature 'GeneSet'
sparseIncidence(x, ...)

## S4 method for signature 'GeneSetCollection'
sparseIncidence(x, ...)

Arguments

`x`	a named list of sets. Elements must be of type `"character"`.
`...`	additional arguments are not currently used.

Details

sparseIncidence differs from GSEABase::incidence in that it returns a sparse matrix, rather than a dense matrix, so it is more memory efficient. It also removes missing elements, removes empty sets, and combines sets with duplicate names.

Value

An object of class dgCMatrix with unique set names as rows and unique elements as columns.

Incidence Matrix

An incidence matrix, $A$ , is defined such that

$A_{ij} = \begin{cases} 1, & \text{if } \text{element } e_j \in \text{set } s_i \\ 0, & \text{otherwise} \end{cases}$

Examples

x <- list("A" = c("a", "b"),
          "A" = c("c"), # duplicate sets
          "B" = c("c", "d"),
          "C" = c("x", "y", "z", "z"), # duplicates
          "D" = c("a", NA)) # missing values

(imat <- sparseIncidence(x))

# Sizes of sets and their pairwise intersections
tcrossprod(imat)

# Number of sets in which each element and pair of elements appears
crossprod(imat)

# Count number of elements unique to each set
keep <- apply(imat, 2, sum) == 1
apply(imat[, keep], 1, sum)

x <- list("A" = c("a", "b"),
          "A" = c("c"), # duplicate sets
          "B" = c("c", "d"),
          "C" = c("x", "y", "z", "z"), # duplicates
          "D" = c("a", NA)) # missing values

(imat <- sparseIncidence(x))

# Sizes of sets and their pairwise intersections
tcrossprod(imat)

# Number of sets in which each element and pair of elements appears
crossprod(imat)

# Count number of elements unique to each set
keep <- apply(imat, 2, sum) == 1
apply(imat[, keep], 1, sum)

Package 'TMSig'

Help Index

Competitive Gene Set Test Accounting for Inter-gene Correlation

Description

Usage

Arguments

Value

Test Assumptions

Author(s)

References

See Also

Examples

Similarity-Based Clustering of Sets

Description

Usage

Arguments

Value

Function Details

Optimization

Minimum Set Size

Source

References

See Also

Examples

Decompose Pairs of Overlapping Sets Into 3 Disjoint Parts

Description

Usage

Arguments

Value

Optimization

Source

References

See Also

Examples

Set Enrichment Bubble Heatmap

Description

Usage

Arguments

Details

Value

See Also

Examples

Color Functions for enrichmap

Description

Usage

Arguments

Details

Value

See Also

Examples

Extend the Range of Values Out to the Nearest Digit

Description

Usage

Arguments

Value

See Also

Examples

Filter a Named List of Sets by Size

Description

Usage

Arguments

Value

Examples

Convert Incidence Matrix to a Named List of Sets

Description

Usage

Arguments

Value

Note

Examples

Invert a List of Sets, Transposing Sets and Elements

Description

Usage

Arguments

Value

Note

Examples

Read GMT File to a Named List of Sets

Description

Usage