gi_list_read {HiCDCPlus} | R Documentation

## gi_list_read

### Description

Reads a written gi_list instance using `gi_list_write` into a valid gi_list instance.

### Usage

    gi_list_read(
      fname,
      chrs = NULL,
      Dthreshold = NULL,
      features = NULL,
      gen = "Hsapiens",
      gen_ver = "hg19"
    )

### Arguments

`fname` | path to the file to read from (can end with .txt, .rds, or .txt.gz).
`chrs` | select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes contained in the `fname`.
`Dthreshold` | maximum distance (included) to check for significant interactions, defaults to the maximum in the data.
`features` | Select the subset of features (1-D or 2-D) to be added to the gi_list instance (without the trailing I or J), defaults to all features (score column gets ingested as 'score').
`gen` | name of the species: e.g., default `'Hsapiens'`
`gen_ver` | genomic assembly version: e.g., default `'hg19'`

### Value

A valid gi_list instance with 1D features stored in regions metadata handle of each list element (e.g., `gi_list[[1]]@regions@elementMetadata`) in the instance and with 2D features stored in metadata handle (i.e., `mcols(gi)`).

### Examples

    outputdir<-paste0(tempdir(check=TRUE),'/')
    gi_list<-generate_binned_gi_list(1e6,chrs='chr22')
    gi_list_write(gi_list,paste0(outputdir,'testgiread.txt'))
    gi_list2<-gi_list_read(paste0(outputdir,'testgiread.txt'))

[Package HiCDCPlus version 1.0.0 Index]