mapToTranscripts() with + and - strand regions
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2.8 years ago
newscient ▴ 20

Hi, Anyone that has been using mapToTranscripts() method from genomicFeatures package and can explain to me the following. I am using it to extract relative position of each position in b within a regions. As:

res <- as.tibble( mapToTranscripts( b.gr,a.gr,ignore.strand=F))

I have a b.gr set with +strand regions and the a.gr regions can either be + strand or - strand. The documentation for the function is:

ignore.strand:  When ignore.strand is TRUE, strand is ignored in overlaps operations (i.e., all strands are considered "+") and the strand in the output is '*'.

When ignore.strand is FALSE strand in the output is taken from the transcripts argument. When transcripts is a GRangesList, all inner list elements of a common list element must have the same strand or an error is thrown.

Mapped position is computed by counting from the transcription start site (TSS) and is not affected by the value of ignore.strand.


From that i understand: By using + b.gr and + a.gr subset with the above command i get mapped position from the TSS to TES (start to end).

But by using the + b.gr and - a.gr subset with the ignore.strand=TRUE option (if this option is not set to TRUE, i get an empty Granges object) will i get mapped position counting from the actual start of the minus transcript(TSS to TES) or the otherway around (TES to TSS)? Meaning if i am going to plot the result will i get the TSS to TES positioning or should i turn the region around in order to get it?

Hopefully I have explained my issue correctly. Thanks in advance

R genome GenomicFeatures • 597 views