gi_list_write: gi_list_write

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

gi_list_write

Description

Writes a valid gi_list instance into a file.

Usage

gi_list_write(
  gi_list,
  fname,
  chrs = NULL,
  columns = "minimal",
  rows = "all",
  significance_threshold = 0.05,
  score = NULL
)

Arguments

gi_list	List of GenomicInteractions objects where each object named with chromosomes contains intra-chromosomal interaction information (see ?gi_list_validate for a detailed explanation of valid gi_list instances).
fname	path to the file to write to (can end with .txt, or .txt.gz).
chrs	select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes in the gi_list.
columns	Can be 'minimal', which is just distance and counts (and HiCDCPlus result columns 'qvalue','pvalue','mu',and 'sdev', if exists; see ?HiCDCPlus) information, 'minimal_plus_features', which is distance, counts, and other calculated 2D features, 'minimal_plus_score', which generates a .hic pre compatible text file, or 'all', which is distance, counts, calculated 2D features, as well as all 1D features. Defaults to 'minimal'.
rows	Can be 'all' or 'significant', which filters rows according to FDR adjusted pvalue column 'qvalue' (this has to exist in mcols(.)) at significance_threshold. Defaults to 'all'.
significance_threshold	Row filtering threshold on 'qvalue'. Defaults to 0.05.
score	Score column to extract to .hic pre compatible file. See mode options in ?hicdc2hic for more details.

Value

a tab separated flat file concatenating all intra-chromosomal interaction information.

Examples

outputdir<-paste0(tempdir(check=TRUE),'/')
gi_list<-generate_binned_gi_list(1e6,chrs='chr22')
gi_list_write(gi_list,paste0(outputdir,'test.txt'))

mervesa/HiCDCPlus documentation built on June 8, 2022, 3:43 a.m.