Hi! I have an IRangesList with several entries like:
[[1]]
IRanges object with 1 range and 8 metadata columns:
start end width | tx_id cds_ok exon_id exon_rank seq_start seq_end
<integer> <integer> <integer> | <character> <logical> <character> <integer> <integer> <integer>
-1 -1 1 | ENST00000281043 <NA> ENSE00000804855 1 16080686 16080760
seq_name seq_strand
<character> <character>
2 *
[[2]]
IRanges object with 1 range and 8 metadata columns:
start end width | tx_id cds_ok exon_id exon_rank seq_start seq_end
<integer> <integer> <integer> | <character> <logical> <character> <integer> <integer> <integer>
-1 -1 1 | ENST00000281043 <NA> ENSE00000804855 1 16080850 16080865
seq_name seq_strand
<character> <character>
2 *
[[3]]
IRanges object with 2 ranges and 8 metadata columns:
start end width | tx_id cds_ok exon_id exon_rank
<integer> <integer> <integer> | <character> <logical> <character> <integer>
ENSP00000373700 1230 1230 1 | ENST00000389048 TRUE ENSE00001154390 24
LRG_488p1 1230 1230 1 | LRG_488t1 TRUE LRG_488t1e24 24
seq_start seq_end seq_name seq_strand
<integer> <integer> <character> <character>
ENSP00000373700 29436905 29436905 2 *
LRG_488p1 29436905 29436905 2 *
[[4]]
IRanges object with 6 ranges and 8 metadata columns:
start end width | tx_id cds_ok exon_id exon_rank
<integer> <integer> <integer> | <character> <logical> <character> <integer>
ENSP00000260795 80 122 43 | ENST00000260795 TRUE ENSE00001164902 2
ENSP00000339824 80 122 43 | ENST00000340107 TRUE ENSE00001164902 3
ENSP00000231803 80 122 43 | ENST00000352904 TRUE ENSE00001164902 2
ENSP00000412903 80 122 43 | ENST00000412135 TRUE ENSE00001164902 3
ENSP00000414914 80 122 43 | ENST00000440486 TRUE ENSE00001164902 3
ENSP00000420533 80 122 43 | ENST00000481110 TRUE ENSE00001164902 3
seq_start seq_end seq_name seq_strand
<integer> <integer> <character> <character>
ENSP00000260795 1801109 1801235 4 *
ENSP00000339824 1801109 1801235 4 *
ENSP00000231803 1801109 1801235 4 *
ENSP00000412903 1801109 1801235 4 *
ENSP00000414914 1801109 1801235 4 *
ENSP00000420533 1801109 1801235 4 *
I would like to remove the entries that are not well mapped (in this case [[1]], and [[2]]) from the IRangesList without performing unlist.
Any ideas? Thanks!
•
written
by
joangibert14 •
## Keep entries where the start coordinate is not (-1):
your.list[unlist(lapply(your.list, function(x) start(x) != -1))]
Is it intentional that you use IRanges instead of GenomicRanges, so no chromosome information? Because that forbids all kinds of intersection operations. Or is the <seq_name> the chromosome?
Hi! Thanks! It worked for me without the unlist function. And yes, <seq_name> gives the chromosome information :).
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