evan199893 / TCGA_expression_clinical_combinator

Use this program can let user quickly combine the miRNA/Gene expression and clinical data. Speed up the data preprocessing step.

TCGA_miRNA_expression_clinical_combinator

1. You should download the expression data and clinical in advanced.
2. Make sure you download the correct metadata.cart.json file on TCGA webpage. In this program will use .json to convert the expression file name. e.g: Project: TCGA-STAD, Data Category: Transcriptome Profiling, Data Type: miRNA-Seq. ##Download on the TCGA page. Should setting correct.
3. You should check wether the the column index is the data you want in the clinical.csv data. (Surival,Stage) In different project may arrange a little differenet. Setting at line #45.
4. Before running the program you should setting the correct absolute path in the specific place.
5. The miRNA/gene expression default is RPKM and takeing log2 in advanced if you don't need that or you need the read count you can change by yourself.(Line #88, 95)
6. I update the program to the user input mode. When you run the program it will ask you to input the specific data file name with absolute path.
7. I upload a R language program about dowaload the raw TCGA data(Gene/miRNA expression and clinical).(TCGA-DLBC)