gi_list_write {HiCDCPlus} | R Documentation

## 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'))

[Package HiCDCPlus version 1.0.0 Index]