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% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/Gene.R
\name{getSegment}
\alias{getSegment}
\alias{getAllele}
\alias{getGene}
\alias{getFamily}
\title{Get Ig segment allele, gene and family names}
\usage{
getSegment(segment_call, segment_regex, first = TRUE, collapse = TRUE,
strip_d = TRUE, omit_nl = FALSE, sep = ",")
getAllele(segment_call, first = TRUE, collapse = TRUE,
strip_d = TRUE, omit_nl = FALSE, sep = ",")
getGene(segment_call, first = TRUE, collapse = TRUE, strip_d = TRUE,
omit_nl = FALSE, sep = ",")
getFamily(segment_call, first = TRUE, collapse = TRUE,
strip_d = TRUE, omit_nl = FALSE, sep = ",")
}
\arguments{
\item{segment_call}{character vector containing segment calls delimited by commas.}
\item{segment_regex}{string defining the segment match regular expression.}
\item{first}{if \code{TRUE} return only the first call in
\code{segment_call}; if \code{FALSE} return all calls
delimited by commas.}
\item{collapse}{if \code{TRUE} check for duplicates and return only unique
segment assignments; if \code{FALSE} return all assignments
(faster). Has no effect if \code{first=TRUE}.}
\item{strip_d}{if \code{TRUE} remove the "D" from the end of gene annotations
(denoting a duplicate gene in the locus);
if \code{FALSE} do not alter gene names.}
\item{omit_nl}{if \code{TRUE} remove non-localized (NL) genes from the result.
Only applies at the gene or allele level.}
\item{sep}{character defining both the input and output segment call
delimiter.}
}
\value{
A character vector containing allele, gene or family names.
}
\description{
\code{getSegment} performs generic matching of delimited segment calls with a custom
regular expression. \link{getAllele}, \link{getGene} and \link{getFamily} extract
the allele, gene and family names, respectively, from a character vector of
immunoglobulin (Ig) or TCR segment allele calls in IMGT format.
}
\examples{
# Light chain examples
kappa_call <- c("Homsap IGKV1D-39*01 F,Homsap IGKV1-39*02 F,Homsap IGKV1-39*01",
"Homsap IGKJ5*01 F")
getAllele(kappa_call)
getAllele(kappa_call, first=FALSE)
getAllele(kappa_call, first=FALSE, strip_d=FALSE)
getGene(kappa_call)
getGene(kappa_call, first=FALSE)
getGene(kappa_call, first=FALSE, strip_d=FALSE)
getFamily(kappa_call)
getFamily(kappa_call, first=FALSE)
getFamily(kappa_call, first=FALSE, collapse=FALSE)
getFamily(kappa_call, first=FALSE, strip_d=FALSE)
# Heavy chain examples
heavy_call <- c("Homsap IGHV1-69*01 F,Homsap IGHV1-69D*01 F",
"Homsap IGHD1-1*01 F",
"Homsap IGHJ1*01 F")
getAllele(heavy_call, first=FALSE)
getAllele(heavy_call, first=FALSE, strip_d=FALSE)
getGene(heavy_call, first=FALSE)
getGene(heavy_call, first=FALSE, strip_d=FALSE)
# Filtering non-localized genes
nl_call <- c("IGHV3-NL1*01,IGHV3-30-3*01,IGHV3-30*01",
"Homosap IGHV3-30*01 F,Homsap IGHV3-NL1*01 F",
"IGHV1-NL1*01")
getAllele(nl_call, first=FALSE, omit_nl=TRUE)
getGene(nl_call, first=FALSE, omit_nl=TRUE)
getFamily(nl_call, first=FALSE, omit_nl=TRUE)
}
\references{
\url{http://imgt.org}
}
\seealso{
\link{countGenes}
}
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