pre-proccessing of RNAseq data for WGCNA

Hi everyone,
i wanted to create an expression matrix for WGCNA input.
however, i has been said that use RPKM/FPKM data instead of CPM, how can i change my TCGA data to RPKM/FPKM in GDCquery and how to filter expression set of genes by FDR to less than 5000, which is ideal for WGCNA as i have 17000 genes in expression set, but i can not add p-value without losing expression set.