Remove entries in a IRangesList

Question

[joangibert14]

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!

Answer 1

[ATpoint]

## 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?

[joangibert14]

Hi! Thanks! It worked for me without the unlist function. And yes, <seq_name> gives the chromosome information :).