R: Get Ig segment allele, gene and family names

getSegment {alakazam} | R Documentation

## 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

### See Also

countGenes

### 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)

[Package alakazam version 0.3.0 Index]