I have a dataset with 88 tumor and 113 normal samples. Among the 50k genes after filtering there are a total of 28k genes (both mRNAs and lncRNAs)
I wanted to do co-expression analysis between lncRNAs and mRNAs to find the targets for each lncRNA. I'm thinking to use WGCNA for co-expression network analysis.
1) For Co-expression network analysis (WGCNA) should I use only tumor samples (or) both tumor and normal samples?
2) If not WGCNA, if I use cor function in R with method Pearson, on what cutoff I should select the target genes?
3) Heard that with bedtools we can know which genes are 10kb upstream/ downstream of lncRNAs to find neighboring pc genes. But no idea how to do that. Could you please give me an example for this.