compMut: Comparison of mutational frequency
In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description Usage Arguments Value References Examples

This function is used to compare mutational frequency among different multi-omics integerative clusters to test the independency between subtypes and mutational status. An oncoprint will be also generated with significant mutations.

compMut(
  moic.res = NULL,
  mut.matrix = NULL,
  freq.cutoff = 0.05,
  test.method = "fisher",
  p.adj.method = "BH",
  doWord = TRUE,
  doPlot = TRUE,
  innerclust = TRUE,
  res.path = getwd(),
  tab.name = NULL,
  fig.path = getwd(),
  fig.name = NULL,
  annCol = NULL,
  annColors = NULL,
  mut.col = "#21498D",
  bg.col = "#dcddde",
  p.cutoff = 0.05,
  p.adj.cutoff = 0.05,
  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
    "#023E8A", "#9D4EDD"),
  width = 8,
  height = 4
)

`moic.res`	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
`mut.matrix`	A binary matrix storing binary mutation data with entries of 0 and 1 only.
`freq.cutoff`	A numeric value to indicate the frequency cutoff for mutation data. Specifically, only features that mutated in over than such proportion would be included in testing; 0.05 by default.
`test.method`	A string value to indicate statistical method for independency testing. Allowed values contain c('fisher', 'chisq'); fisher by default.
`p.adj.method`	A string value to indicate the correction method for multiple comparision. Allowed values contain c('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr'); BH by default.
`doWord`	A logic value to indicate if transformating the .txt outfile to a .docx WORD file (.txt file will be also kept); TRUE by default.
`doPlot`	A logic value to indicate if generating oncoprint; TRUE by default.
`innerclust`	A logic value to indicate if perform clustering within each subtype; TRUE by default.
`res.path`	A string value to indicate the path for saving the table.
`tab.name`	A string value to indicate the name of the output table.
`fig.path`	A string value to indicate the output path for storing the oncoprint.
`fig.name`	A string value to indicate the name of the oncoprint.
`annCol`	A data.frame storing annotation information for samples.
`annColors`	A list of string vectors for colors matched with annCol.
`mut.col`	A string vector to indicate the mutation color for oncoprint.
`bg.col`	A string vector to indicate the background color for oncoprint.
`p.cutoff`	A numeric value to indicate the nominal p value cutoff for significant mutations shown in the oncoprint; 0.05 by default.
`p.adj.cutoff`	A numeric value to indicate the adjusted p value cutoff for significant mutations shown in the oncoprint; 0.05 by default.
`clust.col`	A string vector storing colors for annotating each subtype.
`width`	A numeric value to indicate the width of output figure.
`height`	A numeric value to indicate the height of output figure.

A figure of mutational oncoprint (.pdf) if doPlot = TRUE, a data.frame storing the difference of mutational frequency among different subtypes and a corresponding table in WORD format if doWord = TRUE.

Gu Z, Eils R, Schlesner M (2016). Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics, 32(18):2847–2849.