dot-readAnnotation: read annotation data

Description Usage Arguments Value

Description

read annotation data for windows This is an unexported lowlevel function to read annotations from a file. The file MUST be tab separated and MUST have the following columns:
chromosome: chromosome name
unique_id: unique id of the window
begin: window start co-ordinate
end: window end co-ordinate
strand: strand
gene_id: gene id
gene_name: gene name
gene_type: gene type annotation
gene_region: gene region
Nr_of_region: number of the current region
Total_nr_of_region: total number of regions
window_number: window number

Usage

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.readAnnotation(fname, uniqIds = NULL, asGRange = TRUE,
  checkWindowNumber = TRUE, start0based = TRUE, threads = 10)

Arguments

fname

character, file name/path

uniqIds

character vector, filter stable and keep annotation for these unique ids

asGRange

logical, boolean, whether to reaturn a GRange object or a data.frame object

checkWindowNumber

logical, check window number

start0based

logical, TRUE (default) or FALSE. If TRUE, then the start

threads

numeric, number of threads for fread (default: 10) positions are considered to be 0-based

Value

data.frame or GRanges object


DEWSeq documentation built on Feb. 7, 2020, 2 a.m.