cvCalcSC: cvCalcSC Function

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

cvCalcSC Function

Description

This function allows to calculate Intra-donor variations in single cell data over longitudinal timepoints. The coefficient of variation (CV=SD/mean) is calculated in average expression data in same donor/participant and corresponding user-defined group (like celltype, cluster) across longitudinal timepoints.

Usage

cvCalcSC(
  data_object,
  meanThreshold = NULL,
  cvThreshold = NULL,
  housekeeping_genes = NULL,
  cl = 2,
  fileName = NULL,
  filePATH = NULL
)

Arguments

data_object	Input PALMO S4 object. Contains annotation table and expression matrix or data frame. Rows represent gene/proteins column represents participant samples (same as annotation table Sample column)
meanThreshold	Average expression threshold to filter lowly expressed genes Default is 0.1 (log2 scale)
cvThreshold	Coefficient of variation threshold to select variable and stable genes. Default is 5 for bulk data. Users can use 10-20 for single cell average expression data.
housekeeping_genes	Optional, vector of housekeeping genes. Default is c('ACTB', 'GAPDH')
cl	Number of clusters. Use nCores-1 to run parallel. Default 2
fileName	User-defined file name, Default outputFile
filePATH	User-defined output directory PATH Default, current directory

Value

PALMO object with CV list

Examples

## Not run: 
palmo_obj=cvCalcSC(data_object=palmo_obj, meanThreshold=0.1, cvThreshold=5)

## End(Not run)

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