generate_df_gi_list {HiCDCPlus} | R Documentation

## generate_df_gi_list

### Description

Generates a gi_list instance from a data frame object describing the regions.

### Usage

    generate_df_gi_list(
      df,
      chrs = NULL,
      Dthreshold = 2e+06,
      gen = "Hsapiens",
      gen_ver = "hg19"
    )

### Arguments

`df` | DataFrame with columns named 'chr', 'start', (and optionally 'end', if the regions have gaps) and 1D features with their respective column names.
`chrs` | select a subset of chromosomes' e.g., c('chr21','chr22'). Defaults to all chromosomes specified in `df`.
`Dthreshold` | maximum distance (included) to check for significant interactions, defaults to 2e6 or maximum in the data, whichever is smaller.
`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 genomic features supplied from `df`. Genomic 1D features are stored in the regions metadata handle of each list element (e.g., `gi_list[[1]]@regions@elementMetadata`).

### Examples

    df<-data.frame(chr='chr9',start=seq(1e6,10e6,1e6))
    gi_list<-generate_df_gi_list(df)

[Package HiCDCPlus version 1.0.0 Index]