.readAnnotation {DEWSeq} | R Documentation

## read annotation data

### 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

[Package DEWSeq version 1.6.0 Index]