| 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.
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). |
gff.file <- system.file("extdata/cts/withNovel.forJunctionSeq.gff.gz",package="JctSeqExData2");
#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