xCellAnalysis: The xCell analysis pipeline

View source: R/xCell.R

xCellAnalysisR Documentation

The xCell analysis pipeline

Description

xCellAnalysis Returns the xCell cell types enrichment scores.

Usage

xCellAnalysis(expr, signatures = NULL, genes = NULL, spill = NULL,
  rnaseq = TRUE, file.name = NULL, scale = TRUE, alpha = 0.5,
  save.raw = FALSE, parallel.sz = 4, parallel.type = "SOCK",
  cell.types.use = NULL)

Arguments

expr

the gene expression data set. A matrix with row names as symbols and columns as samples.

signatures

a GMT object of signatures.

genes

list of genes to use in the analysis.

spill

the Spillover object for adjusting the scores.

rnaseq

if true than use RNAseq spillover and calibration paramters, else use array parameters.

file.name

string for the file name for saving the scores. Default is NULL.

scale

if TRUE, uses scaling to trnasform scores using fit.vals

alpha

a value to override the spillover alpha parameter. Deafult = 0.5

save.raw

TRUE to save a raw

parallel.sz

integer for the number of threads to use. Default is 4.

parallel.type

Type of cluster architecture when using snow. 'SOCK' or 'FORK'. Fork is faster, but is not supported in windows.

cell.types.use

a character list of the cell types to use in the analysis. If NULL runs xCell with all cell types. The spillover compensation step may over compensate, thus it is always better to run xCell with a list of cell types that are expected to be in the mixture. The names of cell types in this list must be a subset of the cell types that are inferred by xCell.

Value

the adjusted xCell scores


dviraran/xCell documentation built on May 3, 2024, 7:17 p.m.