alakazam (version 0.2.2)

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, mode = c("gene",
  "allele", "family"))

Arguments

data

data.frame with Change-O style columns containing clonal assignments.

gene

column containing allele assignments. Only the first allele in the column will be considered.

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.

mode

one of c("gene", "family", "allele") defining the degree of specificity regarding allele calls. Determines whether to return counts for genes, families or alleles.

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 thecopycolumn. for each gene. Only present if thecopyargument is specified.
  • COPY_FREQ: frequency of the gene as a fraction of the total copy number within each group. Only present if thecopyargument is specified.
  Additional columns defined by the groups argument will also be present.

Examples

# Load example data
file <- system.file("extdata", "ExampleDb.gz", package="alakazam")
df <- readChangeoDb(file)

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

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