summarizeRows: Summarizing rows/columns by a factor

In ribiosUtils: Utilities from and Interface to the Bioinfo-C (BIOS) Library

Description

Apply a function to summarize rows/columns that assigned to the same level by a factor vector.

Usage

summarizeRows(matrix, factor, fun = mean, ...)

Arguments

matrix	A numeric matrix
factor	A vector of factors, either of the length of nrow(matrix) (for summarizeRows), or the length of ncol(matrix) (for summarizeColumns).
fun	A function or a name for a function, the summarizing function applied to rows/columns sharing the same level
...	Further parameters passed to the function

Details

NA levels are neglected, and corresponding rows/columns will not contribute to the summarized matrix.

summarizeCols is synonymous to summarizeColumns

Value

A matrix, the dimension will be determined by the number of levels of the factor vector.

Author(s)

Jitao David Zhang <[e-mail]>

Examples

my.matrix <- matrix(1:25, nrow=5)
print(my.matrix)

my.factor <- factor(c("A", "B", "A", "C", "B"))
summarizeRows(matrix=my.matrix, factor=my.factor, fun=mean)
summarizeRows(matrix=my.matrix, factor=my.factor, fun=prod)
summarizeColumns(matrix=my.matrix, factor=my.factor, fun=mean)
summarizeColumns(matrix=my.matrix, factor=my.factor, fun=prod)

## NA values in factor
my.na.factor <- factor(c("A", "B", "A", "C", NA))
summarizeRows(matrix=my.matrix, factor=my.na.factor, fun=mean)
summarizeRows(matrix=my.matrix, factor=my.na.factor, fun=prod)
summarizeColumns(matrix=my.matrix, factor=my.na.factor, fun=mean)
summarizeColumns(matrix=my.matrix, factor=my.na.factor, fun=prod)

ribiosUtils documentation built on March 13, 2020, 2:54 a.m.