atac2rna: Convert a peak matrix to a gene activity matrix
In cailab-tamu/scTypeGSEA: Single Cell Type Gene Set Enrichment Analysis

Description Usage Arguments Value Examples

This function takes in a peak matrix and an annotation file (gtf)and collapse the peak matrix to a gene activity matrix.

atac2rna(
  peaks,
  annotation.file = NULL,
  seq.levels = c(1:22, "X", "Y"),
  include.body = TRUE,
  upstream = 2000,
  downstream = 0
)

`peaks`	Matrix of peak counts.
`annotation.file`	Path to GTF annotation file.
`seq.levels`	Which seqlevels to keep (corresponds to chromosomes usually).
`include.body`	Include the gene body?
`upstream`	Number of bases upstream to consider.
`downstream`	Number of bases downstream to consider.

A Seurat object with both ATAC data matrix and gene activity matrix.

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## Not run: annotation.file <- "../data/Homo_sapiens.GRCh37.82.gtf"
         ATAC_example <- atac2rna(pbmc_small_atac, annotation.file = annotation.file)
## End(Not run)