Subsetting ranged data with its values.
Example
subset reads according to the width
> paired.read.rd
RangedData with 997111 rows and 1 value column across 1 space
space ranges | strand
|
1 chr4 [ 146855, 146898] | +
2 chr4 [1322462, 1322493] | -
3 chr4 [ 135547, 135703] | +
4 chr4 [ 965138, 965228] | -
5 chr4 [ 614464, 614606] | +
6 chr4 [ 274244, 274297] | +
7 chr4 [1191851, 1191994] | -
8 chr4 [ 310251, 310393] | +
9 chr4 [ 524981, 525273] | +
... ... ... ... ...
997103 chr4 [1071785, 1071930] | -
997104 chr4 [ 819270, 819409] | -
997105 chr4 [ 951987, 952139] | +
997106 chr4 [ 327573, 327659] | -
997107 chr4 [ 343265, 343289] | -
997108 chr4 [ 615827, 615992] | +
997109 chr4 [ 615402, 615423] | -
997110 chr4 [ 128254, 128323] | +
997111 chr4 [ 659492, 659641] | -
> paired.read.rd[width(paired.read.rd) > 100, ]
RangedData with 623327 rows and 1 value column across 1 space
space ranges | strand
|
1 chr4 [ 135547, 135703] | +
2 chr4 [ 614464, 614606] | +
3 chr4 [1191851, 1191994] | -
4 chr4 [ 310251, 310393] | +
5 chr4 [ 524981, 525273] | +
6 chr4 [1174028, 1174189] | -
7 chr4 [1174480, 1174655] | +
8 chr4 [ 869049, 869191] | -
9 chr4 [ 595415, 595565] | +
... ... ... ... ...
623319 chr4 [ 646433, 646588] | +
623320 chr4 [ 227923, 228078] | -
623321 chr4 [1204606, 1204767] | -
623322 chr4 [1013562, 1013741] | -
623323 chr4 [1071785, 1071930] | -
623324 chr4 [ 819270, 819409] | -
623325 chr4 [ 951987, 952139] | +
623326 chr4 [ 615827, 615992] | +
623327 chr4 [ 659492, 659641] | -
Or subset() works, too.
Leave a Reply