getSegment

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 = ","
)

getLocus(
segment_call,
first = TRUE,
collapse = TRUE,
strip_d = TRUE,
omit_nl = FALSE,
sep = ","
)

getChain(
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¶

https://www.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"
[2] "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"


getLocus(kappa_call)

[1] "IGK" "IGK"

getChain(kappa_call)

[1] "VL" "VL"


# 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"              
[3] "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"


getFamily(heavy_call)

[1] "IGHV1" "IGHD1" "IGHJ1"

getLocus(heavy_call)

[1] "IGH" "IGH" "IGH"

getChain(heavy_call)

[1] "VH" "VH" "VH"


# 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"              
[3] ""

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" ""


# Temporary designation examples
tmp_call <- c("IGHV9S3*01", "IGKV10S12*01")

getAllele(tmp_call)

[1] "IGHV9S3*01"   "IGKV10S12*01"

getGene(tmp_call)

[1] "IGHV9S3"   "IGKV10S12"

getFamily(tmp_call)

[1] "IGHV9"  "IGKV10"