Question: correlation between PCGs and the neighboring lncRNAs using LINC
0
17 months ago by
edoardobertolini0 wrote:

Hello!

I'm trying to correlate the expression of PCGs and the adjacent lncRNAs within the same tissue using TPM values. My input is a matrix 496 TPM of one column where the first 256 rows are lncRNAs and the remaining are PCGs. Gene names are specified as rownames.

What is the best approach? I tried the bioconductor package LINC with the function linc() giving as input the matrix here attached and the TRUE/FALSE vertor but I got an error

Thanks

Ed

This is the input matrix:

str(input)

num [1:496, 1] 15.4 7.6 50.9 24.9 17.6 ...
- attr(*, "dimnames")=List of 2
..$: chr [1:496] "MSTRG.2537.1" "MSTRG.11169.1" "MSTRG.27321.1" "MSTRG.13970.1" ... ..$ : chr "V1"