addFeatureStats: Add feature statistics

In splatter: Simple Simulation of Single-cell RNA Sequencing Data

Description

Add additional feature statistics to a SingleCellExperiment object

Usage

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

Arguments

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.

Details

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.

Value

SingleCellExperiment with additional feature statistics

splatter documentation built on Dec. 3, 2020, 2:01 a.m.