Count circRNA host gene expression from given BED6 format CircCoordinates.
1 2 | HostGeneCount(CircCoordinates, bamfiles, ncore = 2, stranded = "unstranded",
splicedOnly = TRUE)
|
CircCoordinates |
CircCoordinates output of DCC, or any other BED6 format files, input as data.frame |
bamfiles |
A iterable list of bamfiles with full path. |
ncore |
Number of core to use. |
stranded |
Whether the library is prepared strand specific, default "unstranded". Accepted values are "unstranded","fs","ss", meaning "unstranded library", "first strand library" and "second strand library" respectively. |
splicedOnly |
Only count reads that are spliced at the circRNA junction, default TRUE. |
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