PALMO (version 0.1.2)

cvCalcSCProfile: 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
)

Value

PALMO object with CV profile list

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

Examples

if (FALSE) {
palmo_obj <- cvCalcSCProfile(data_object=palmo_obj,
housekeeping_genes=c('GAPDH', 'ACTB'), fileName='scrna')
}