StableFeatures: StableFeatures Function

In aifimmunology/PALMO: Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

StableFeatures Function

Description

This function allows user to identify stable genes in participants across longitudinal timepoints using single cell expression data. The coefficient of variation (CV) calculated using cvCalcSC function. Users can identify cvThreshold in different datasets using housekeeping genes CV distribution.

Usage

StableFeatures(
  data_object,
  group_oi = NULL,
  cvThreshold = NULL,
  donorThreshold = NULL,
  housekeeping_genes = NULL,
  groupThreshold = NULL,
  topFeatures = 25,
  filePATH = NULL,
  fileName = NULL
)

Arguments

data_object	Input PALMO S4 object. It contains annotation information and expression data from Bulk or single cell data.
group_oi	Group of interest to focus on. Example among celltypes focus on selected ones. Default is NULL.
cvThreshold	Coefficient of variation threshold to select variable and stable genes Default is 10 for single cell RNA (100*SD/mean)
donorThreshold	Donor threshold number to be used, Default is number of participants
housekeeping_genes	Optional list of housekeeping genes to focus on. Default is ACTB, GAPDH
groupThreshold	Group label threshold number to be used, Default is (number of participants x group labels)/2
topFeatures	Number of features to be selected from each group, Default is 25
filePATH	User-defined output directory path to load the CV result obtained from cvCalcSC function
fileName	User defined filename

Value

PALMO object with stable (stable_genes) features

Examples

## Not run: 
palmo_obj <- StableFeatures(data_object=palmo_obj, cvThreshold=10)

## End(Not run)

aifimmunology/PALMO documentation built on Oct. 21, 2022, 7:39 p.m.