dot-readAnnotation: read annotation data

In DEWSeq: Differential Expressed Windows Based on Negative Binomial Distribution

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

.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 Nov. 28, 2020, 2:01 a.m.