compFGA: Comparison of fraction genome altered

In xlucpu/MOVICS: Multi-Omics integration and VIsualization in Cancer Subtyping

Description

This function calculates Fraction Genome Altered (FGA), Fraction Genome Gained (FGG), and Fraction Genome Lost (FGL) seperately, and compares them among curent subtypes identified from multi-omics integrative clustering algorithms.

Usage

compFGA(
  moic.res = NULL,
  segment = NULL,
  iscopynumber = FALSE,
  cnathreshold = 0.2,
  test.method = "nonparametric",
  barcolor = c("#008B8A", "#F2042C", "#21498D"),
  clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627",
    "#023E8A", "#9D4EDD"),
  fig.path = getwd(),
  fig.name = NULL,
  width = 8,
  height = 4
)

Arguments

moic.res	An object returned by 'getMOIC()' with one specified algorithm or 'get%algorithm_name%' or 'getConsensusMOIC()' with a list of multiple algorithms.
segment	A data frame containing segmented copy number and columns must exactly include the following elements: c('sample','chrom','start','end','value'). Column of 'value' should be segments value when iscopynumber = FALSE but copy-number value when iscopynumber = TRUE. Copy-number will be converted to segments by log2(copy-number/2).
iscopynumber	A logical value to indicate if the fifth column of segment input is copy-number. If segment file derived from CNV calling provides copy number instead of segment_mean value, this argument must be switched to TRUE. FALSE by default.
cnathreshold	A numeric value to indicate the cutoff for identifying copy-number gain or loss. 0.2 by default.
test.method	A string value to indicate the method for statistical testing. Allowed values contain c('nonparametric', 'parametric'); nonparametric means two-sample wilcoxon rank sum test for two subtypes and Kruskal-Wallis rank sum test for multiple subtypes; parametric means two-sample t-test when only two subtypes are identified, and anova for multiple subtypes comparison; "nonparametric" by default.
barcolor	A string vector to indicate the mapping color for bars of FGA, FGG and FGL.
clust.col	A string vector storing colors for each subtype.
fig.path	A string value to indicate the output path for storing the barplot.
fig.name	A string value to indicate the name of the barplot.
width	A numeric value to indicate the width of barplot.
height	A numeric value to indicate the height of barplot.

Value

A list contains the following components:

summary a table summarizing the measurements of FGA, FGG, and FGL per sample

FGA.p.value a nominal p value quantifying the difference of FGA among current subtypes

pairwise.FGA.test a pairwise BH adjusted p value matrix for multiple comparisons of FGA if more than 2 subtypes were identified

FGG.p.value a nominal p value quantifying the difference of FGG among current subtypes

pairwise.FGG.test a pairwise BH adjusted p value matrix for multiple comparisons of FGG if more than 2 subtypes were identified

FGL.p.value a nominal p value quantifying the difference of FGL among current subtypes

pairwise.FGL.test a pairwise BH adjusted p value matrix for multiple comparisons of FGL if more than 2 subtypes were identified

test.method a string value indicating the statistical testing method to calculate p values

References

Cerami E, Gao J, Dogrusoz U, et al. (2012). The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer Discov, 2(5):401-404.

Gao J, Aksoy B A, Dogrusoz U, et al. (2013). Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal, 6(269):pl1-pl1.

Examples

# There is no example and please refer to vignette.

xlucpu/MOVICS documentation built on July 24, 2021, 9:23 p.m.