HostGeneCount: HostGeneCount

Description Usage Arguments

Description

Count circRNA host gene expression from given BED6 format CircCoordinates.

Usage

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HostGeneCount(CircCoordinates, bamfiles, ncore = 2, stranded = "unstranded",
  splicedOnly = TRUE)

Arguments

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.


dieterich-lab/CircTest documentation built on May 15, 2019, 8:29 a.m.