tcR (version 2.1.1)

geneUsage: Gene usage.

Description

Compute frequencies or counts of gene segments ("V / J - usage").

Usage

geneUsage(.data, .genes = HUMAN_TRBV_MITCR, .quant = c(NA, "read.count",
  "umi.count", "read.prop", "umi.prop"), .norm = F, .ambig = F)

Arguments

.data

Cloneset data frame or a list with clonesets.

.genes

Either one of the gene alphabet (e.g., HUMAN_TRBV, genealphabets) or list with two gene alphabets for computing joint distribution.

.quant

Which column to use for the quantity of clonotypes: NA for computing only number of genes without using clonotype counts, "read.count" for the "Read.count" column, "umi.count" for the "Umi.count" column, "read.prop" for the "Read.proportion" column, "umi.

.norm

If T then return proportions of resulting counting of genes.

.ambig

If F than remove from counting genes which are not presented in the given gene alphabet(s).

Value

• If .data is a cloneset and .genes is NOT a list than return a data frame with first column "Gene" with genes and second with counts / proportions.

  If .data is a list with clonesets and .genes is NOT a list than return a data frame with first column "Gene" with genes and other columns with counts / proportions for each cloneset in the input list.

  If .data is a cloneset and .genes IS a list than return a matrix with gene segments for the first gene in .genes and column names for the second gene in .genes. See "Examples".

  If .data is a list with clonesets and .genes IS a list than return a list with matrices like in the previous case.

See Also

genealphabets, vis.gene.usage, pca.segments

Examples

# Load your data
data(twb)
# compute V-segments frequencies of human TCR beta.
seg <- geneUsage(twb, HUMAN_TRBV, .norm = T)
# plot V-segments frequencies as a heatmap
vis.heatmap(seg, .labs = c("Sample", "V gene"))
# plot V-segments frequencies directly from clonesets
vis.gene.usage(twb, HUMAN_TRBV)
# plot V-segments frequencies from the gene frequencies
vis.gene.usage(seg, NA)
# Compute V-J joint usage.
geneUsage(twb, list(HUMAN_TRBV, HUMAN_TRBJ))