chromNames2integers: Rename chromosomes

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Rename chromosomes

Description

Rename chromosomes into integers, especially useful with FImpute, GEMMA, qqman, SNPRelate, etc.

Usage

chromNames2integers(
  x,
  basic = FALSE,
  prefix = "chr",
  toreplace2 = "_random",
  prefix2 = NULL,
  thresh.max.chr.int = +Inf
)

Arguments

x	vector of chromosome names (if factor, will be converted to character)
basic	if TRUE, the unique chromosome identifiers will be sorted alphanumerically (which requires gtools), and will be renamed as 1, ..., nb of chromosomes (for SNPRelate)
prefix	characters to be removed at the start of each chromosome name (case will be ignored)
toreplace2	second set of characters to be removed in chromosome names (start or end), especially useful for "random" chromosomes (case will be ignored)
prefix2	second prefix to be removed at the start of each chromosome name for those for which "prefix" didn't work (case will be ignored)
thresh.max.chr.int	threshold on the maximum chromosome integer, above which the renaming will simply be the sequence from 1 to the number of chromosomes

Value

data frame with the same length as x, and two columns named "original" and "renamed"

Author(s)

Timothee Flutre

Examples

## Not run: ## example from grapevine
chroms <- c("chr1", "chr1_random", "chr10", "chr10_random", "chrUn", "chr2")
chromNames2integers(x=chroms)

## example from apple
chroms <- c("Chr15", "Chr01", "Chr02", "Chr00", "Chr02")
chromNames2integers(x=chroms)

## example from cherry
chroms <- c("Super-Scaffold_14", "Super-Scaffold_4374", "Super-Scaffold_27")
chromNames2integers(x=chroms, prefix="Super-Scaffold_",
                    thresh.max.chr.int=500)

## example from apricot
chroms <- c("Pp08", "scaffold_51", "Pp02", "Pp01", "scaffold_23")
chromNames2integers(x=chroms, prefix="Pp", toreplace2=NULL,
                    prefix2="scaffold_")

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.