BloodBrainCorrelation

Testing for correlations between expression in the blood and brain

Tanya Phung's script

1. Rename tissue ID in TPM file to sample ID

• Rename tissue ID in TPM file to sample ID in order to select the individuals that have TPM values when comparing 2 tissues
• Use the script rename_tpm.py:

  python rename_tpm.py -h
  usage: rename_tpm.py [-h] --infile INFILE --outfile OUTFILE
  
  Rename tissue ID in TPM file to sample ID
  
  optional arguments:
  -h, --help         show this help message and exit
  --infile INFILE    Input the path to the infile. This file is the file after
                     running subset_tpm.py. Example is Blood_tpm.tsv
  --outfile OUTFILE  Input the path to the output file where the tissue ID is
                     renamed to sample ID
  

  • Example:

  python rename_tpm.py --infile Blood_tpm.tsv --outfile Blood_tpm_sampleID.tsv
  python rename_tpm.py --infile Putamen_tpm.tsv --outfile Putamen_tpm_sampleID.tsv
  

2. Subset the tissue tpm files to contain samples that are shared between 2 tissues

• Use the script subset_tissue_tpm_for_shared_samples.py:

  python subset_tissue_tpm_for_shared_samples.py -h
  usage: subset_tissue_tpm_for_shared_samples.py [-h] --tissue_1_tpm
                                               TISSUE_1_TPM --tissue_2_tpm
                                               TISSUE_2_TPM
                                               --tissue_1_tpm_shared
                                               TISSUE_1_TPM_SHARED
                                               --tissue_2_tpm_shared
                                               TISSUE_2_TPM_SHARED
  
  Subset tissue tpm files to contain samples that are shared between 2 tissues
  
  optional arguments:
  -h, --help            show this help message and exit
  --tissue_1_tpm TISSUE_1_TPM
                        Input the path to tissue 1 tpm file after renaming.
                        For example: Blood_tpm_sampleID.tsv
  --tissue_2_tpm TISSUE_2_TPM
                        Input the path to tissue 2 tpm file after renaming.
                        For example: Putamen_tpm_sampleID.tsv
  --tissue_1_tpm_shared TISSUE_1_TPM_SHARED
                        Input the output file for tissue 1 that contains
                        shared samples
  --tissue_2_tpm_shared TISSUE_2_TPM_SHARED
                        Input the output file for tissue 2 that contains
                        shared samples
  

  • Example:

  python subset_tissue_tpm_for_shared_samples.py --tissue_1_tpm Blood_tpm_sampleID.tsv --tissue_2_tpm Putamen_tpm_sampleID.tsv --tissue_1_tpm_shared Blood_tpm_sampleID_shared_Blood.tsv --tissue_2_tpm_shared Putamen_tpm_sampleID_shared_Putamen.csv
  

  • In addition to 2 new output files Blood_tpm_sampleID_shared_Blood.tsv and Putamen_tpm_sampleID_shared_Putamen.csv, this script prints out:

  Number of shared samples is  160
  Number of columns of tissue 1 after subsetting for shared samples is  162
  Number of columns of tissue 2 after subsetting for shared samples is  162
  

  • So you know that the number of shared samples match.

3. Subset genes with certain tpm threshold

• Use the script subset_genes_with_tpm_threshold.py:

python subset_genes_with_tpm_threshold.py -h
usage: subset_genes_with_tpm_threshold.py [-h] --tpm_threshold TPM_THRESHOLD
                                        --tissue_1_tpm TISSUE_1_TPM
                                        --tissue_2_tpm TISSUE_2_TPM
                                        --tissue_1_out TISSUE_1_OUT
                                        --tissue_2_out TISSUE_2_OUT

Subset genes with certain tpm threshold

optional arguments:
-h, --help            show this help message and exit
--tpm_threshold TPM_THRESHOLD
                      Input the value for the tpm threshold. For example: 1
--tissue_1_tpm TISSUE_1_TPM
                      Input the path to tissue 1 tpm. For example:
                      Blood_tpm_sampleID_shared_Putamen.tsv
--tissue_2_tpm TISSUE_2_TPM
                      Input the path to tissue 2 tpm. For example:
                      Putamen_tpm_sampleID_shared_Blood.tsv
--tissue_1_out TISSUE_1_OUT
                      Input the path to tissue 1 output that contains only
                      genes where tpm across all samples is greater than
                      threshold.
--tissue_2_out TISSUE_2_OUT
                      Input the path to tissue 2 output that contains only
                      genes where tpm across all samples is greater than
                      threshold.

• Example:

python subset_genes_with_tpm_threshold.py --tpm_threshold 1 --tissue_1_tpm Blood_tpm_sampleID_shared_Blood.tsv --tissue_2_tpm Putamen_tpm_sampleID_shared_Putamen.tsv --tissue_1_out Blood_tpm_sampleID_shared_Blood_genes_tpm_greater_than_1.tsv --tissue_2_out Putamen_tpm_sampleID_shared_Putamen_genes_tpm_greater_than_1.tsv

• This script also prints out:

Number of genes with tpm greater than threshold of  1.0  is:  3243