estimateSizeFactorsForMatrix {DESeq} | R Documentation |
Given a matrix or data frame of count data, this function estimates the size factors as follows: Each column is divided by the geometric means of the rows. The median (or, ir requested, another location estimator) of these ratios (skipping the genes with a geometric mean of zero) is used as the size factor for this column.
Typically, you will not call this function directly, but use estimateSizeFactors
.
estimateSizeFactorsForMatrix( counts, locfunc=median)
counts |
a matrix or data frame of counts, i.e., non-negative integer values |
locfunc |
a function to compute a location for a sample. By default, the median is used. However,
especially for low counts, the |
a vector with the estimates size factors, one element per column
Simon Anders, sanders@fs.tum.de
cds <- makeExampleCountDataSet() estimateSizeFactorsForMatrix( counts(cds) )