meth_array/Scripts_description.txt at master · Joshmoss11/meth_array · GitHub

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Description for scripts in /cs/icore/joshua.moss/scripts/meth_array_scripts/summary_scripts directory:

1. process array data from idats - one script for all (TCGA/GEO/lab_data)
Desc:
process idats data - noob, BMIQ, remove sex chromosomes and more.

Scripts:
process_array.R
process_array.csh
process_queue.csh - runs with one param - Data source (TCGA/GEO/lab_data) (40 minutes run)

2. Create cancer queue or tissue queue
Desc:
creates cancer_queue in TCGA dr or tissue_queue files in GEO/lab_data dir

Scripts:
create_cancer_queue_TCGA.R - runs with one param - the path to save queue file
create_tissue_queue.R - runs with one param - the path to save queue file

3. Group data by cancer type fo TCGA, or Group by tissue type for GEO/lab_data
Scripts:
group_by_cancer_type_TCGA.R
group_by_cancer_type_TCGA.csh
group_by_cancer_queue_TCGA.csh - no params needed (32 minutes run)

group_by_tissue_type.R
group_by_tissue_type.csh
group_by_tissue_queue.csh - runs with one param - Data source (GEO/lab_data) (2 minutes run) knows to deal with 450,850 rows

4. Sum data by cancer type for TCGA - means, std, quantile 0.1, quantile 0.9, samples_num
Scripts:
summary_scripts/sum_by_cancer_TCGA.R
summary_scripts/sum_by_cancer_TCGA.csh
summary_scripts/sum_by_cancer_queue_TCGA.csh - no params needed (50 minutes run)

5. Sum data by tissue type GEO/lab_data - means, std, quantile 0.1, quantile 0.9, samples_num
Scripts:
summary_scripts/sum_by_tissue.R
summary_scripts/sum_by_tissue.csh
summary_scripts/sum_by_tissue_queue.csh  - runs with one param - Data source (GEO/lab_data) (5 minutes run)

6. Sum data by statistics TCGA
Desc:
Rearrange all means in one csv, all std in one csv...

Scripts:
summary_scripts/sum_by_statistics_TCGA.R
summary_scripts/sum_by_statistics_TCGA.csh
summary_scripts/sum_by_stat_TCGA.csh - no params needed (4 minutes run)

7. Sum data by statistics lab_data/GEO
Desc:
Rearrange all means in one csv, all std in one csv... works on data of 450000 and 850000 rows

Scripts:
summary_scripts/sum_by_statistics.R
summary_scripts/sum_by_statistics.csh
summary_scripts/sum_by_stat.csh - runs with one param - Data source (GEO/lab_data) (4 minutes run)