collapse_genes: Select probe sets to represent genes

In csbl-usp/collapseR: Collapse and filter tables

Description

Select a "probe set" to represent each "gene" choosing those with highest or lowest mean expression level (see details in method).

Usage

collapse_genes(x, id_col = NULL, genes = NULL, method = c("maxMean",
  "minMean"), drop = character(), df = FALSE)

Arguments

x	A matrix, data frame or data table.
id_col	Column name of identifiers column (key column).
genes	A vector of length nrow(x) of the "genes" identifiers or a mapping of probes to genes (an object coercible to a data table with "probes" identifiers in the first column and "genes" identifiers in the second). In this last case, x should have its "probes" identifiers in the id_col column or in its row names.
method	Method to choose the "probe set" representative of a "gene": the one with maximum row mean ('maxMean') or with minimum row mean ('minMean'). Defaults to "maxMean".
drop	Columns to drop (before summarizing and from result).
df	Return a data frame instead of a data table. Defaults to FALSE.

Value

Table with unique observations for each "gene".

See Also

collapse_replicates

csbl-usp/collapseR documentation built on May 6, 2019, 8:32 p.m.