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, 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

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.
omit_nl
if TRUE remove non-localized (NL) genes from the result. Only applies at the gene or allele level.
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

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)

[1] "IGKV1-39*01" "IGKJ5*01"   

getAllele(kappa_call, first=FALSE)

[1] "IGKV1-39*01,IGKV1-39*02" "IGKJ5*01"               

getAllele(kappa_call, first=FALSE, strip_d=FALSE)

[1] "IGKV1D-39*01,IGKV1-39*02,IGKV1-39*01" "IGKJ5*01"                            


getGene(kappa_call)

[1] "IGKV1-39" "IGKJ5"   

getGene(kappa_call, first=FALSE)

[1] "IGKV1-39" "IGKJ5"   

getGene(kappa_call, first=FALSE, strip_d=FALSE)

[1] "IGKV1D-39,IGKV1-39" "IGKJ5"             


getFamily(kappa_call)

[1] "IGKV1" "IGKJ5"

getFamily(kappa_call, first=FALSE)

[1] "IGKV1" "IGKJ5"

getFamily(kappa_call, first=FALSE, collapse=FALSE)

[1] "IGKV1,IGKV1,IGKV1" "IGKJ5"            

getFamily(kappa_call, first=FALSE, strip_d=FALSE)

[1] "IGKV1D,IGKV1" "IGKJ5"       


# 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)

[1] "IGHV1-69*01" "IGHD1-1*01"  "IGHJ1*01"   

getAllele(heavy_call, first=FALSE, strip_d=FALSE)

[1] "IGHV1-69*01,IGHV1-69D*01" "IGHD1-1*01"               "IGHJ1*01"                


getGene(heavy_call, first=FALSE)

[1] "IGHV1-69" "IGHD1-1"  "IGHJ1"   

getGene(heavy_call, first=FALSE, strip_d=FALSE)

[1] "IGHV1-69,IGHV1-69D" "IGHD1-1"            "IGHJ1"             


# 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)

[1] "IGHV3-30-3*01,IGHV3-30*01" "IGHV3-30*01"               ""                         

getGene(nl_call, first=FALSE, omit_nl=TRUE)

[1] "IGHV3-30-3,IGHV3-30" "IGHV3-30"            ""                   

getFamily(nl_call, first=FALSE, omit_nl=TRUE)
[1] "IGHV3" "IGHV3" "IGHV1"

See also

countGenes