countGenes - Tabulates V(D)J allele, gene or family usage.

Description

Determines the count and relative abundance of V(D)J alleles, genes or families within groups.

Usage

countGenes(data, gene, groups = NULL, copy = NULL, clone = NULL,
mode = c("gene", "allele", "family", "asis"))

Arguments

data
data.frame with Change-O style columns.
gene
column containing allele assignments. Only the first allele in the column will be considered when mode is “gene”, “family” or “allele”. The value will be used as it is with mode="asis".
groups
columns containing grouping variables. If NULL do not group.
copy
name of the data column containing copy numbers for each sequence. If this value is specified, then total copy abundance is determined by the sum of copy numbers within each gene. This argument is ignored if clone is specified.
clone
name of the data column containing clone identifiers for each sequence. If this value is specified, then genes will be counted only once for each clone. Note, this is accomplished by using the most common gene within each clone identifier. As such, ambiguous alleles within a clone will not be accurately represented.
mode
one of c("gene", "family", "allele", "asis") defining the degree of specificity regarding allele calls. Determines whether to return counts for genes (calling getGene), families (calling getFamily), alleles (calling getAllele) or using the value as it is in the column gene, without any processing.

Value

A data.frame summarizing family, gene or allele counts and frequencies with columns:

  • GENE: name of the family, gene or allele
  • SEQ_COUNT: total number of sequences for the gene.
  • SEQ_FREQ: frequency of the gene as a fraction of the total number of sequences within each grouping.
  • COPY_COUNT: sum of the copy counts in the copy column. for each gene. Only present if the copy argument is specified.
  • COPY_FREQ: frequency of the gene as a fraction of the total copy number within each group. Only present if the copy argument is specified.
  • CLONE_COUNT: total number of clones for the gene.
  • CLONE_FREQ: frequency of the gene as a fraction of the total number of clones within each grouping.

Additional columns defined by the groups argument will also be present.

Examples

# Without copy numbers
genes <- countGenes(ExampleDb, gene="V_CALL", groups="SAMPLE", mode="family")
genes <- countGenes(ExampleDb, gene="V_CALL", groups="SAMPLE", mode="gene")
genes <- countGenes(ExampleDb, gene="V_CALL", groups="SAMPLE", mode="allele")

# With copy numbers and multiple groups
genes <- countGenes(ExampleDb, gene="V_CALL", groups=c("SAMPLE", "ISOTYPE"), 
copy="DUPCOUNT", mode="family")

# Count by clone
genes <- countGenes(ExampleDb, gene="V_CALL", groups=c("SAMPLE", "ISOTYPE"), 
clone="CLONE", mode="family")