Updated mtp tables qc checks to include expression tpm tables

[ewafula]

What analysis module should be updated and why?

Update mutation-frequencies-table-checks

What changes need to be made? Please provide enough detail for another participant to make the update.

1. Rename module to mtp-tables-qc-checks from mutation-frequencies-table-checks
2. Copy the v11 long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz and long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz tables from rna-seq-expression-summary-stats module to module current/ directory
3. Copy the v10 long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz and long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz tables from rna-seq-expression-summary-stats module to module previous/ directory
4. Create 02-tpm-tables-checks.Rmd to QC the long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz and long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz. Can adapt code for tpm QC check from 01-frequencies-tables-checks.Rmd script for mutation frequencies QC checks
5. Update the run_frequencies-tables-checks.sh bash script to include running the new 02-tpm-tables-checks.Rmd script
6. Update README accordingly

What input data should be used?

• long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz
• long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz

What are the expected new output files?

• long_n_tpm_mean_sd_quantile_gene_wise_zscore.nb.html
• long_n_tpm_mean_sd_quantile_group_wise_zscore.nb.html
• results/long_n_tpm_mean_sd_quantile_gene_wise_zscore.xlsx
• results/long_n_tpm_mean_sd_quantile_group_wise_zscore.xlsx

When do you expect the revised analysis will be completed?

Current sprint

Who will complete the updated analysis?

@adilahiri

[ewafula]

@logstar, where can I get the v10 long_n_tpm_mean_sd_quantile_gene_wise_zscore.tsv.gz and long_n_tpm_mean_sd_quantile_group_wise_zscore.tsv.gz tables that you sue for API plotting. Need to use for this ticket to compare v10 vs v11.1.