Integration of TCGA and CCLE data

Download TCGA clinical/subtype information

Move to transcriptomic_data/ and start R
```
$ cd transcriptomic_data
$ R
```
Read integration.R
```
source("integration.R")
```
Run outputClinical() or outputSubtype()
```
outputClinical("BRCA")
outputSubtype("BRCA")
```
Output: <TCGA Study Abbreviation>_clinic.csv or <TCGA Study Abbreviation>_subtype.csv

Select samples in reference to clinical or subtype data

You can select the patient’s state based on the clinical or subtype data obtained above.

patientSelection(type = subtype,
                 ID = "patient",
                 pathologic_stage %in% c("Stage_I", "Stage_II"),
                 age_at_initial_pathologic_diagnosis < 60)

Download TCGA gene expression data (HTSeq-Counts)

Download the gene expression data of the specified sample types (Sample Type Codes) in the cancer type specified by outputClinical() or outputSubtype(). By running this code, you can get data of only the patients selected by sampleSelection().
```
downloadTCGA(cancertype = "BRCA",
             sampletype = c("01", "06"),
             outputresult = FALSE)
```
Output: Number of selected samples

Download CCLE transcriptomic data

Download CCLE transcriptomic data. You can select cell lines derived from one specific cancer type.
```
downloadCCLE(cancertype = "BREAST",
             outputresult = FALSE)
```
Output: Number of selected samples

Merge TCGA and CCLE data

Merge TCGA data download with downloadTCGA() and CCLE data download with downloadCCLE().
Run ComBat-seq program to remove batch effects between TCGA and CCLE datasets.
Output total read counts of all samples in order to decide the cutoff value of total read counts for normalization().
```
mergeTCGAandCCLE(outputesult = FALSE)
```
Output : totalreadcounts.csv

Normalize RNA-seq counts data

Conduct normalization of RNA-seq.
You can specify min and max value for truncation of total read counts.
If you do not want to specify values for truncation, please set min=F or max=F.
```
normalization(min=40000000, max=140000000)
```
Output : TPM_RLE_postComBat_<TCGA>_<CCLE>.csv