Add additional feature statistics to a SingleCellExperiment object
addFeatureStats( sce, value = c("counts", "cpm", "tpm", "fpkm"), log = FALSE, offset = 1, no.zeros = FALSE )
sce | SingleCellExperiment 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 SingleCellExperiment. |
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. |
SingleCellExperiment with additional feature statistics
Currently adds the following statistics: mean, variance, coefficient of
variation, median and median absolute deviation. Statistics are added to
the rowData
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
analysis packages.