countGenes {alakazam}R Documentation

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


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


  groups = NULL,
  copy = NULL,
  clone = NULL,
  fill = FALSE,
  mode = c("gene", "allele", "family", "asis"),
  remove_na = TRUE



data.frame with AIRR-format or Change-O style columns.


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".


columns containing grouping variables. If NULL do not group.


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.


name of the data column containing clone identifiers for each sequence. If this value is specified, then one gene will be considered 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.


logical of c(TRUE, FALSE) specifying when if groups (when specified) lacking a particular gene should be counted as 0 if TRUE or not (omitted)


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.


removes rows with NA values in the gene column if TRUE and issues a warning. Otherwise, keeps those rows and considers NA as a gene in the final counts and relative abundances.


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

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


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

# With copy numbers and multiple groups
genes <- countGenes(ExampleDb, gene="v_call", groups=c("sample_id", "c_call"), 
                    copy="duplicate_count", mode="family")

# Count by clone
genes <- countGenes(ExampleDb, gene="v_call", groups=c("sample_id", "c_call"), 
                    clone="clone_id", mode="family")

# Count absent genes 
genes <- countGenes(ExampleDb, gene="v_call", groups="sample_id", 
                    mode="allele", fill=TRUE)

[Package alakazam version 1.1.0 Index]