cvSCsampleprofile: cvSCsampleprofile Function

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

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
)

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

Value

PALMO object with CV list

Examples

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

## End(Not run)

PALMO documentation built on Aug. 18, 2022, 1:06 a.m.