Find top genes that correlate with my gene of interest using TCGA RNA-Seq data and CCLE data in R.

Question

[Dila]

Hi everyone . I know some basics i R. I want to use R to find the top genes whose expression correlates with my gene of interest using TCGA RNA-Seq datasets and CCLE datasets to generate a figure depicting the correlation. I take tcga and ccle data and ı make normalization and filtering. It looks like this. How can I make table then correlation afterthat. Can you help me?

[Hamid Ghaedi]

If you are looking for correlation coefficients, then calculating the correlation matrix would be an option:

# df is a data frame with numerical values with no missing
res <-  cor(t(df))

[Dila]

I get nothing from this code. I want to find top genes that correlate with my gene of interest using TCGA RNA-Seq data and CCLE data in R. This data TCGA brca cancer data. First column is include all genes. I can't select my gene of interest to find correlated genes. What should I do?

[Hamid Ghaedi]

The code is not a 'plug and play' one. Why you don't post your effort (code) in R here so more help from more people you would get once they see your efforts. P.S the gene names are in row names and NOT a column. rownames(df) would return a character vector of gene names.