load_peaks {chipenrich} | R Documentation |
Given a data.frame
in BEDX+Y format, use the built-in function
GenomicRanges::makeGRangesFromDataFrame()
to convert to GRanges
.
load_peaks(dframe, keep.extra.columns = TRUE)
dframe |
A BEDX+Y style |
keep.extra.columns |
Keep extra columns parameter from |
Typically, this function will not be used alone, but inside chipenrich()
.
A GRanges
that may or may not keep.extra.columns
, and
that may or may not be stranded, depending on whether there is strand column
in the dframe
.
# Example with just chr, start, end peaks_df = data.frame( chr = c('chr1','chr2','chr3'), start = c(35,74,235), end = c(46,83,421), stringsAsFactors = FALSE) peaks = load_peaks(peaks_df) # Example with extra columns peaks_df = data.frame( chr = c('chr1','chr2','chr3'), start = c(35,74,235), end = c(46,83,421), strand = c('+','-','+'), score = c(36, 747, 13), stringsAsFactors = FALSE) peaks = load_peaks(peaks_df, keep.extra.columns = TRUE)