| readAnnotationData {JunctionSeq} | R Documentation |
This function reads the "flattened" gff annotation file created by QoRTs.
This annotation file contains all the gene, transcript, exon, and junction ID's and their loci.
In general this function is not used by the end-user, but is called internally by
runJunctionSeqAnalyses or readJunctionSeqCounts.
readAnnotationData(flat.gff.file)
flat.gff.file |
Character string. The filename of the "flat" gff annotation file. The file may be gzip-compressed. This "flat" gff file must be produced by the QoRTs jar utility using the makeFlatGtf or mergeNovelSplices functions (depending on whether inclusion of novel splice junctions is desired). |
A data.frame object, containing the annotation information from the flat gff file.
gff.file <- system.file("extdata/cts/withNovel.forJunctionSeq.gff.gz",
package="JctSeqData");
#Parse the GFF file:
annoData <- readAnnotationData(gff.file);
head(annoData);
## featureName featureType chrom start end strand
## 1 ENSRNOG00000050954:E001 exonic_part chr14 182677 183555 -
## 2 ENSRNOG00000050954:E002 exonic_part chr14 184706 184830 -
## 3 ENSRNOG00000050954:E003 exonic_part chr14 186228 186453 -
## 4 ENSRNOG00000050954:E004 exonic_part chr14 189145 189973 -
## 5 ENSRNOG00000050954:E005 exonic_part chr14 190012 190189 -
## 6 ENSRNOG00000050954:E006 exonic_part chr14 190205 190293 -
## gene_id part_number transcripts
## 1 ENSRNOG00000050954 001 ENSRNOT00000073973
## 2 ENSRNOG00000050954 002 ENSRNOT00000073973
## 3 ENSRNOG00000050954 003 ENSRNOT00000073973
## 4 ENSRNOG00000050954 004 ENSRNOT00000073973
## 5 ENSRNOG00000050954 005 ENSRNOT00000073973
## 6 ENSRNOG00000050954 006 ENSRNOT00000073973