Entering edit mode
Hello,
Can someone help me to subset each first intron (only) from a GRangesList representing intronsByTranscript? I've been somewhat out of practice for a period of time, and I'm stuck. Thanks,
tx
TxDb object:
# Db type: TxDb
# Supporting package: GenomicFeatures
# Data source: GCA_007735645.1
# Organism: Venturia.effusa
# Taxonomy ID: 50376
# miRBase build ID: NA
# Genome: ASM773564v1
# Nb of transcripts: 10897
# Db created by: GenomicFeatures package from Bioconductor
# Creation time: 2024-02-01 11:28:21 -0500 (Thu, 01 Feb 2024)
# GenomicFeatures version at creation time: 1.52.1
# RSQLite version at creation time: 2.3.1
# DBSCHEMAVERSION: 1.2
intr<-intronsByTranscript(tx)
intr
GRangesList object of length 10897:
$`1`
GRanges object with 0 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
-------
seqinfo: 21 sequences from ASM773564v1 genome
$`2`
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] CP042185.1 102664-102719 +
-------
seqinfo: 21 sequences from ASM773564v1 genome
$`3`
GRanges object with 1 range and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] CP042185.1 114417-114472 +
-------
seqinfo: 21 sequences from ASM773564v1 genome
...
<10894 more elements>
> intr[10400]
GRangesList object of length 1:
$`10400`
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] CP042202.1 614609-614653 -
[2] CP042202.1 615053-615568 -
-------
seqinfo: 21 sequences from ASM773564v1 genome
> la<-lapply(intr,"[[",1)
Error in getListElement(x, i, ...) :
GRanges objects don't support [[, as.list(), lapply(), or unlist() at the
moment