removeNAs: removeNAs

In CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

Description

Removing NA from snp data.

Usage

removeNAs(snp.data, lrr.na = TRUE, baf.na = TRUE, id.na = TRUE, verbose = TRUE)

Arguments

snp.data	(GRanges, GRangesList or list) A GRanges, GRangesList or a list of GRanges.
lrr.na	(logical) Whether to remove the rows that have NAs in the lrr column. (defaults to TRUE)
baf.na	(logical) Whether to remove the rows that have NAs in the baf column. (defaults to TRUE)
id.na	(logical) Whether to remove the rows that have NAs in the id column. (defaults to TRUE)
verbose	(logical) Whether to show information messages. (defaults to TRUE)

Details

This function will remove rows with NA values in snp data. We can decide which columns we take into account to detect NAs, using the lrr.na, baf.na and id.na parameters.

Value

A GRanges or a list of GRanges where the NA values have been removed.

Examples

#GRanges
seg.data <- regioneR::toGRanges(data.frame(chr = c("chr1", "chr1", "chr2", "chr5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(NA,0.25,1.5,NA)))
seg.data <- removeNAs(snp.data = seg.data)

#List of GRanges
seg.data <- list(a = regioneR::toGRanges(data.frame(chr = c("chr1", "chr1", "chr2", "chr5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(NA,0.25,1.5,NA),baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))),
                    b=regioneR::toGRanges(data.frame(chr = c("chr1", "chr1", "chr2", "chr5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(2.5,NA,1.5,0.25), baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))))
seg.data <- removeNAs(snp.data = seg.data)

#GRangesList
seg.data <- GRangesList(a = regioneR::toGRanges(data.frame(chr = c("chr1", "chr1", "chr2", "chr5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(NA,0.25,1.5,NA), baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))), b=regioneR::toGRanges(data.frame(chr = c("chr1", "chr1", "chr2", "chr5"), start = c(0,50000,8014630,14523572), end = c(48953, 7023664,9216331,153245687), lrr = c(2.5,NA,1.5,0.25), baf = c(1.5,2.5,NA,6), id = c("rs52456","rs52457","rs52458","rs52459"))))
seg.data <- removeNAs(snp.data = seg.data)

CopyNumberPlots documentation built on Nov. 8, 2020, 6:51 p.m.