Entering edit mode
Hello!
I am working with SummarizedExperiment that contain genomis data. I want to extract a certaimn part of this sequence, but only if it is encoded on the reverse strand. I am using the code below but that doesnt work. When I exclude the if argument, everything works and I get the result I was looking for but when I try to include the condition, it fails. Can someone explain to me what I am doing wrong?
#**Test1:**
GRanges(
seqnames(data1),
if (rowRanges(data1)@strand == "-")
{
IRanges(
start(data1$nc_end),
end(data1)
},
strand(data1))
#**Test2**
GRanges(
seqnames(data1),
if (data1@strand == "-")
{
IRanges(
start(data1$nc_end),
end(data1)
},
strand(data1))
Results of R Session1
Error in MatrixGenerics:::.load_next_suggested_package_to_search(x) : Failed to find a rowRanges() method for GRanges objects.
Results of R Session2
Error in if (includedExonsLMI@strand == "+") { : argument is not interpretable as logical
I can't reproduce your issue because you did not provided an example of your dataset (example with
dput(head(data1)), but in the first case you use rowRanges() which require an input of type "matrix, array, or numeric" (https://rdrr.io/bioc/MatrixGenerics/man/rowRanges.html). In the second case, there is a missing parenthesis which doesn't close the IRanges() function so it cannot work.I'm not sure I understand what you're trying to do.
ifshould evaluate a scalar, it looks like you're using a vector. Perhaps useifelseand/or rethink the whole operation. If you already have aGRanges, use the typical subsetting operations based on the conditional vector that you provide to theiffunction.As always, please provide a fully reproducible example including the expected output.
Best,
Marcel