loadCopyNumberCalls: loadCopyNumberCalls

In bernatgel/CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

loadCopyNumberCalls

Description

Loads copy number calls from a tabular format

Usage

loadCopyNumberCalls(cnv.data, chr.col = NULL, start.col = NULL, end.col = NULL, cn.col = NULL, loh.col = NULL, segment.value.col = NULL, genome = NULL, zero.based = FALSE, verbose = TRUE)

Arguments

cnv.data	Either the name of the file with the data or a variable containing the data
chr.col	(number or character) The name or number of the column with chromosome information. If NULL, it is automatically identified. (defaults to NULL)
start.col	(number or character) The name or number of the column with start position information. If NULL, it is automatically identified. (defaults to NULL)
end.col	(number or character) The name or number of the column with end position information. If NULL, it is automatically identified. (defaults to NULL)
cn.col	(number or character) The name or number of the column with CN information. If NULL, it is automatically identified. (defaults to NULL)
loh.col	(number or character) The name or number of the column with LOH information. If NULL, it is automatically identified. (defaults to NULL)
segment.value.col	(number or character) The name or number of the column with segment value. If NULL, it is automatically identified. (defaults to NULL)
genome	(character) The name of the genome (defaults to NULL)
zero.based	(logical) Whether the data is zero-based and half open (i.e. ranges are defined by (start:end] so chr1:10-20 represents nine bases long features spanning from base 11 to 20). (defaults to FALSE)
verbose	(logical) Whether to show information messages. (defaults to TRUE)

Details

This function will load segments data from any "bed-like" data structure in R or file. Internally it uses the toGRanges function from regioneR package and can work with any format accepted by it, including R objects and local or remote files. If no column names are specified, it will use simple heuristics to try to identify the relevant data columns.

Value

A GRanges with a range per copy number segment

Examples

df <- data.frame("id"= "rs1234","chromosome"="chr1", "Start"=0, "end.position"=100,
"copy.number.level"=3, "LOH"=0, "median.value.per.segment"=1.2,
"BAF"=0.2, "Log Ratio"=1.5, "strange.name"="strange.value")

cnv.call <- loadCopyNumberCalls(cnv.data = df) 

bernatgel/CopyNumberPlots documentation built on Sept. 22, 2023, 1:53 a.m.