PALMO (version 0.1.2)

StableFeatures: 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
)

Value

PALMO object with stable (stable_genes) features

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

Examples

if (FALSE) {
palmo_obj <- StableFeatures(data_object=palmo_obj, cvThreshold=10)
}