PALMO (version 0.1.2)

cvSCsampleprofile: cvSCsampleprofile Function

Description

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

Usage

cvSCsampleprofile(
  data_object,
  meanThreshold = NULL,
  cvThreshold = NULL,
  cl = 2,
  plot_log10 = FALSE,
  fileName = NULL,
  filePATH = NULL
)

Value

PALMO object with CV 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)

cvThreshold

Coefficient of variation threshold to select variable and stable genes Default is 10 for single cell RNA (100*SD/mean)

cl

Number of clusters. Use nCores-1 to run parallel. Default 2

plot_log10

Optional, Plot CV vs Mean on log10 scale. Default FALSE

fileName

User-defined file name, Default outputFile

filePATH

User-defined output directory PATH Default, current directory

Examples

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