removeNAs {CopyNumberPlots} | R Documentation

## removeNAs

### 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)

[Package CopyNumberPlots version 1.3.3 Index]