mostVariable {SQMtools}

Get the N most variable rows (or columns) from a numeric table

Description

Return a subset of an input matrix or data frame, containing only the N most variable rows (or columns), sorted. Variability is calculated as the Coefficient of Variation (sd/mean).

Usage

mostVariable(data, N = 10, bycol = FALSE)

Arguments

data

numeric matrix or data frame

N

integer Number of rows to return (default 10).

bycol

logical. Operate on columns instead of rows (default FALSE).

Value

A matrix or data frame (same as input) with the selected rows or columns.

Examples

data(Hadza)
Hadza.carb = subsetFun(Hadza, "Carbohydrate metabolism")
# Which are the 20 most variable KEGG functions in the ORFs related to carbohydrate metabolism?
topCarb = mostVariable(Hadza.carb$functions$KEGG$tpm, N=20)
# Now print them with nice names
rownames(topCarb) = paste(rownames(topCarb),
                          Hadza.carb$misc$KEGG_names[rownames(topCarb)], sep="; ")
topCarb
# We can pass this to any R function
heatmap(topCarb)
# But for convenience we provide wrappers for plotting ggplot2 heatmaps and barplots
plotHeatmap(topCarb, label_y="TPM")
plotBars(topCarb, label_y="TPM")