generate_df_gi_list: generate_df_gi_list

In mervesa/HiCDCPlus: Hi-C Direct Caller Plus

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)

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