Question: problem with makeGRangesListFromFeatureFragments
0
gravatar for mariamari693693
2.4 years ago by
mariamari6936930 wrote:

Hi,

I want to convet :

myFile.txt

======

MotifName       strand  targetName      targetStart     targetEnd
GATA1   *       chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1    48847536,127527717,102379250,140094948,113485701,28285784,119187237,178110784,105353030,1206548448848140,127528321,102379672,140095753,113486305,28286388,119187841,178111113,105353634,12065981

 

to a GRangesList in R:

library(GenomicRanges)
dat <- read.table("myFile.txt",header=TRUE, stringsAsFactors=FALSE)

grl2 <- with(dat,
             makeGRangesListFromFeatureFragments(seqnames=Rle(factor(targetName)),
                                                 fragmentStarts=targetStart,
                                                 fragmentEnds=targetEnd,
                         strand=strand,
                         sep=","
                                                 ))
names(grl2) <- dat$MotifName

But it does not work. It get:

> grl2
GRangesList object of length 1:
$GATA1
GRanges object with 10 ranges and 0 metadata columns:
                                                   seqnames
                                                      <Rle>
   [1] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [2] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [3] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [4] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [5] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [6] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [7] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [8] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
   [9] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
  [10] chr15,chr7,chrX,chr9,chr2,chr18,chr3,chr5,chr12,chr1
                       ranges strand
                    <IRanges>  <Rle>
   [1] [ 48847536,  48848140]      *
   [2] [127527717, 127528321]      *
   [3] [102379250, 102379672]      *
   [4] [140094948, 140095753]      *
   [5] [113485701, 113486305]      *
   [6] [ 28285784,  28286388]      *
   [7] [119187237, 119187841]      *
   [8] [178110784, 178111113]      *
   [9] [105353030, 105353634]      *
  [10] [ 12065484,  12065981]      *

-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths

 

if I do not collapse chr in original file:

myFile2.txt:

MotifName       strand  targetName      targetStart     targetEnd
GATA1   *       chr4    159756456,6910762       159757078,6911248
GATA1   *       chr1    87230642        87231449
GATA1   *       chr12   34175051        34175655
GATA1   *       chr8    100135438       100135841
GATA1   *       chr12   31478801        31479405
GATA1   *       chr20   45989193        45989872
GATA1   *       chr13   45289893,37573340       45290497,37573944
GATA1   *       chr9    127150856       127151460

> grl2
GRangesList object of length 8:
$GATA1
GRanges object with 2 ranges and 0 metadata columns:
      seqnames                 ranges strand
         <Rle>              <IRanges>  <Rle>
  [1]     chr4 [159756456, 159757078]      *
  [2]     chr4 [  6910762,   6911248]      *

$GATA1
GRanges object with 1 range and 0 metadata columns:
      seqnames               ranges strand
  [1]     chr1 [87230642, 87231449]      *

$GATA1
GRanges object with 1 range and 0 metadata columns:
      seqnames               ranges strand
  [1]    chr12 [34175051, 34175655]      *

...
<5 more elements>
-------
seqinfo: 7 sequences from an unspecified genome; no seqlengths


I get multiple GATA1, which I do not want and would like only one $GATA1 contains all chrs, starts and ends

Thanks for helping me to solve this problem

 

ADD COMMENTlink modified 2.3 years ago by shepherl ♦♦ 1.3k • written 2.4 years ago by mariamari6936930
Answer: problem with makeGRangesListFromFeatureFragments
0
gravatar for shepherl
2.3 years ago by
shepherl ♦♦ 1.3k
United States
shepherl ♦♦ 1.3k wrote:

You should be able to use unlist and split to get the results you want. If you unlist the grl2 made from myFile2.txt the names on the
GRangesList should become the rownames; then split on rowname if you want a GRangesList split by motif name.

 

ADD COMMENTlink written 2.3 years ago by shepherl ♦♦ 1.3k

But it would make sense for makeGRangesListFromFeatureFragments() to support collapsed seqnames.

ADD REPLYlink written 2.3 years ago by Michael Lawrence10k
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