Add additional feature statistics to an SCESet object

addFeatureStats(sce, value = c("counts", "cpm", "tpm", "fpkm"), log = FALSE,
  offset = 1, no.zeros = FALSE)

Arguments

sce

SCESet to add feature statistics to.

value

the expression value to calculate statistics for. Options are "counts", "cpm", "tpm" or "fpkm". The values need to exist in the given SCESet.

log

logical. Whether to take log2 before calculating statistics.

offset

offset to add to avoid taking log of zero.

no.zeros

logical. Whether to remove all zeros from each feature before calculating statistics.

Value

SCESet with additional feature statistics

Details

Currently adds the following statistics: mean, variance, coefficient of variation, median and median absolute deviation. Statistics are added to the fData slot and are named Stat[Log]Value[No0] where Log and No0 are added if those arguments are true. UpperCamelCase is used to differentiate these columns from those added by scater.