sortDFByGene: Sort data frame by genes

In williamdlees/vdjbasevis: multiple visualizations for genotypes

Description

sortDFByGene Sort the data.frame by the genes names or position. For sorting by gene names the sortAlleles function by TIgGER is used. For sorting by position the defualt package gene location list is used.

Usage

sortDFByGene(
  DATA,
  chain = c("IGH", "IGK", "IGL"),
  method = c("name", "position"),
  removeIGH = FALSE,
  geno = FALSE,
  peseudo_remove = F,
  ORF_remove = F
)

Arguments

DATA	data frame to sort
chain	the Ig chain: IGH,IGK,IGL. Default is IGH.
method	the method for sorting the genes. If by 'name' the genes in the output are ordered lexicographically, if by 'position' only functional genes are used and are ordered by their chromosomal location. Default is 'position'.
removeIGH	if TRUE, 'IGH'\'IGK'\'IGL' prefix is removed from gene names.

Value

sorted data.frame

williamdlees/vdjbasevis documentation built on Sept. 13, 2020, 12:17 a.m.