reduceCrossTab: Reduce 'crossTab'.

In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description

Reduce the input contingency table by associating sequences with KEGG Pathway, KEGG Module or COG functional category identifiers.

Usage

reduceCrossTab(x, target)

## S4 method for signature 'crossTab,character'
reduceCrossTab(x, target)

Arguments

x	A crossTab object to be reduced.
target	Character vector indicating which onthology to use, either "pathway" or "module", or "cogfunction".

Value

Returns input crossTab object, with updated contingency table, displaying new category values in rows, and updated counts in columns.

Examples

# create contingency table
s <- getKO(HD59)
v <- as.numeric(MELP(HD59, ribosomal = TRUE))
ct <- crossTab(s, v)
ct

# reduce contingency table
reduceCrossTab(ct, "pathway")
reduceCrossTab(ct, "module")

coRdon documentation built on Nov. 8, 2020, 5:28 p.m.