cvCalcSCProfile: cvCalcSCProfile Function

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

cvCalcSCProfile Function

Description

This function allows to calculate Intra-donor variations in single cell data over longitudinal timepoints and visualize in a CV vs Mean plot. Plots stored in output directory.

Usage

cvCalcSCProfile(
  data_object,
  meanThreshold = 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)
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 profile list

Examples

## Not run: 
palmo_obj <- cvCalcSCProfile(data_object=palmo_obj,
housekeeping_genes=c('GAPDH', 'ACTB'), fileName='scrna')

## End(Not run)

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