gtfToBed: Extract the Chromosomal Information Required in bed Format...
In GenomicTools: Collection of Tools for Genomic Data Analysis
Description
Usage
Arguments
Details
Value
Author(s)
Examples
Description
This function creates a matrix of gene annotations in bed format, based on the information given in an importet gtf table.
Usage
1
Arguments
gtf
An imported gtf table.
correctBases
Logical subtract 1 from bases
Details
After a gtf file was imported with importGTF this function transforms it into a data.frame with bed formatting.
The option correctBases adjusts the coordinates in the bed object according to the bed standard. The base counting
in gtf starts with 1, wheras in bed-files they start with 0.
Value
A data.frame in bed format having the four columns Chr, Start, Stop and Gene
Author(s)
Daniel Fischer
Examples
1
2
3
4
5
## Not run:
annotTrack <- read.table(file="Homo_sapiens.GRCh37.70.gtf",sep="\t")
annotBed <- gtfToBed(annotTrack)
## End(Not run)
GenomicTools documentation built on March 13, 2020, 3:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) Examples
Description
This function creates a matrix of gene annotations in bed format, based on the information given in an importet gtf table.
Usage
1 |
Arguments
gtf |
An imported gtf table. |
correctBases |
Logical subtract 1 from bases |
Details
After a gtf file was imported with importGTF this function transforms it into a data.frame with bed formatting.
The option correctBases adjusts the coordinates in the bed object according to the bed standard. The base counting
in gtf starts with 1, wheras in bed-files they start with 0.
Value
A data.frame in bed format having the four columns Chr, Start, Stop and Gene
Author(s)
Daniel Fischer
Examples
1 2 3 4 5 | ## Not run:
annotTrack <- read.table(file="Homo_sapiens.GRCh37.70.gtf",sep="\t")
annotBed <- gtfToBed(annotTrack)
## End(Not run)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.