xCellAnalysis: The xCell analysis pipeline
In alex-pinto/xc: Cell type enrichment analysis

Description Usage Arguments Value

xCellAnalysis Returns the xCell cell types enrichment scores.

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

`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.