Create gene activity matrix
Compute counts per cell in gene body and promoter region.
GeneActivity( object, assay = NULL, features = NULL, extend.upstream = 2000, extend.downstream = 0, biotypes = "protein_coding", max.width = 5e+05, verbose = TRUE, ... )
object |
A Seurat object |
assay |
Name of assay to use. If NULL, use the default assay |
features |
Genes to include. If NULL, use all protein-coding genes in the annotations stored in the object |
extend.upstream |
Number of bases to extend upstream of the TSS |
extend.downstream |
Number of bases to extend downstream of the TTS |
biotypes |
Gene biotypes to include. If NULL, use all biotypes in the gene annotation. |
max.width |
Maximum allowed gene width for a gene to be quantified. Setting this parameter can avoid quantifying extremely long transcripts that can add a relatively long amount of time. If NULL, do not filter genes based on width. |
verbose |
Display messages |
... |
Additional options passed to |
Returns a sparse matrix
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
fragments <- CreateFragmentObject(
path = fpath,
cells = colnames(atac_small),
validate.fragments = FALSE
)
Fragments(atac_small) <- fragments
GeneActivity(atac_small)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.