cvCalcBulk: cvCalcBulk Function

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

cvCalcBulk Function

Description

This function allows to calculate Intra-donor variations in bulk data over longitudinal timepoints. The coefficient of variation (CV=SD/mean) is calculated in Bulk data in same donor/participant across timepoints.

Usage

cvCalcBulk(
  data_object,
  meanThreshold = 1,
  cvThreshold = 5,
  median_cvThreshold = NULL,
  donorThreshold = NULL,
  housekeeping_genes = NULL,
  naThreshold = 1,
  plot_log10 = FALSE,
  selectedFeatures = NULL,
  median_cv_max = NULL,
  plotWidth = 5,
  plotHeight = 8,
  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 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.
median_cvThreshold	Optional, median of CVs from each donor/participant calculated. Threshold used to differentiate variable and stable features across donors/participants. Default, same as cvThreshold.
donorThreshold	Donor threshold number to be used, Default is number of participants
housekeeping_genes	Optional, vector of housekeeping genes. Default is c("ACTB", "GAPDH")
naThreshold	Optional, For a give feature % of donors/participants showing non-NA CVs (NAs appear due to expression ~0 or absent). Default is 1 means all donors/participants to consider. 0.5 means from 4 donors atleast 2 donors should have non-NA CVs for a given feature.
plot_log10	Optional, Plot CV vs Mean on log10 scale. Default FALSE
selectedFeatures	Optional, focus on selected genes/features.
median_cv_max	Optional, Remove features with greater than median CV Default is NULL
plotWidth	Optional, heat plot width 5 in
plotHeight	Optional, heat plot height 8 in
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=cvCalcBulk(data_object=palmo_obj, meanThreshold=0.1, cvThreshold=5)

## End(Not run)

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