freq.p.test: Obtains significance cutoff for the frequency of binary...

Description Usage Arguments Value Examples

View source: R/freq.p.test.r

Description

Obtains significance cutoff for the frequency of binary events encoded in a matrix

Usage

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freq.p.test(
  mat,
  method = "fdr",
  p.cut = 0.05,
  iter = 100,
  zerofreq = TRUE,
  plot = TRUE,
  verbose = TRUE
)

Arguments

mat

(numeric matrix) a binary matrix where columns will be tested for their sum value compared to a permutated matrix

method

(character) the method to pass to p.adjust function

p.cut

(numeric) the cutoff for multiple hypothesis corrected p.value

iter

(numeric) Number of iterations to produce null distribution (note that null size will be iter*ncol(mat))

zerofreq

(logical) whether to remove bins with observed frequency = 0; It is recommended to set to TRUE when the bins span genomic regions of low coverage

plot

(logical) whether to generate a histogram comparing observed and null frequency distributions

Value

an instance of the class 'freq.cut'

Examples

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## validate input data.frames
cnv <- validate.cnv(segdat_lung_ccle)

## obtain a matrix of genomic bins vs samples indicating high density of breaks
shatt.regions <- shattered.regions.cnv(cnv)
mat <- shatt.regions@high.density.regions.hc

freq.p.test(mat)

gonzolgarcia/svcnvplus documentation built on March 4, 2020, 6:02 p.m.