[R] calculate correlations

[Elham -]

Hi All,I have 11 human RNA-seq data (control/treatment),The effect of various drugs on various cancers,I want to calculate the genes-lncRna correlations for all tumors considered together for network,I did differential expression analysis and prepared normalized values (rpkm) of coding and lncoding in two separate file and import them to R, then transpose them and now I want to calculate corr by this function:
control.corr=cor(cod[grep(".C",cod$name),-1],lnc[grep(".C",lnc$name),-1],method = "spearman")

if I understand true,I should write the numbers of columns whose related to control,then I counted all of control`s column and wrote 23 .now my question is,how does R understand what column is control and what is treatment?


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