alakazam (version 0.2.2)

getSegment: Get Ig segment allele, gene and family names

Description

getSegment performs generic matching of delimited segment calls with a custom regular expression. getAllele, getGene and getFamily extract the allele, gene and family names, respectively, from a character vector of immunoglobulin (Ig) or TCR segment allele calls in IMGT format.

Usage

getSegment(segment_call, segment_regex, first = TRUE, collapse = TRUE,
  strip_d = TRUE, sep = ",")
getAllele(segment_call, first = TRUE, collapse = TRUE, strip_d = TRUE,
  sep = ",")
getGene(segment_call, first = TRUE, collapse = TRUE, strip_d = TRUE,
  sep = ",")
getFamily(segment_call, first = TRUE, collapse = TRUE, strip_d = TRUE,
  sep = ",")

Arguments

segment_call

character vector containing segment calls delimited by commas.

segment_regex

string defining the segment match regular expression.

first

if TRUE return only the first call in segment_call; if FALSE return all calls delimited by commas.

collapse

if TRUE check for duplicates and return only unique segment assignments; if FALSE return all assignments (faster). Has no effect if first=TRUE.

strip_d

if TRUE remove the "D" from the end of gene annotations (denoting a duplicate gene in the locus); if FALSE do not alter gene names.

sep

character defining both the input and output segment call delimiter.

Value

• A character vector containing allele, gene or family names.

References

http://imgt.org

See Also

Other sequence annotation functions: extractVRegion

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_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)