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Updated analysis: tumor-gtex-plots - collapse tables #119

Closed jharenza closed 3 years ago

jharenza commented 3 years ago

What analysis module should be updated and why?

tumor-gtex-plots

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

FNL would like two long tables for each analysis type (cohort+cancer_group and cancer_group). The tables should look something like this (eg for cancer_group table, for which we will use all_cohorts as the cohort):

gene ENSG_id cohort cancer_group x_labels mean median sd efo_code mondo_code uberon_code plot_api
GPC2 all_cohorts Neuroblastoma Neuroblastoma (N = 211) 27.57 26.32 15.88 X_api
GPC2 all_cohorts Neuroblastoma Adipose - Subcutaneous (N = 663) 1.76 1.66 0.82 X_api
GPC2 all_cohorts Neuroblastoma Adipose - Visceral (Omentum) (N = 541) 1.2 1.04 0.65 X_api
GPC2 all_cohorts Neuroblastoma Adrenal Gland (N = 258) 0.72 0.63 0.36 X_api
GPC2 all_cohorts Neuroblastoma Artery - Aorta (N = 432) 1.45 1.3 0.74 X_api
GPC2 all_cohorts Neuroblastoma Artery - Coronary (N = 240) 1.37 1.14 0.95 X_api
GPC2 all_cohorts Neuroblastoma Artery - Tibial (N = 663) 0.75 0.61 0.59 X_api
GPC2 all_cohorts Neuroblastoma Bladder (N = 21) 1.98 1.85 1.25 X_api
GPC2 all_cohorts Neuroblastoma Brain - Amygdala (N = 152) 2.29 2.22 0.86 X_api
GPC2 all_cohorts Neuroblastoma Brain - Anterior cingulate cortex (BA24) (N = 176) 1.86 1.78 0.65 X_api
GPC2 all_cohorts Neuroblastoma Brain - Caudate (basal ganglia) (N = 246) 1.35 1.35 0.5 X_api
GPC2 all_cohorts Neuroblastoma Brain - Cerebellar Hemisphere (N = 215) 3.12 2.79 1.83 X_api
GPC2 all_cohorts Neuroblastoma Brain - Cerebellum (N = 241) 3.27 2.77 1.98 X_api
GPC2 all_cohorts Neuroblastoma Brain - Cortex (N = 255) 1.63 1.53 0.57 X_api
GPC2 all_cohorts Neuroblastoma Brain - Frontal Cortex (BA9) (N = 209) 1.61 1.56 0.59 X_api
GPC2 all_cohorts Neuroblastoma Brain - Hippocampus (N = 197) 2.21 2.09 1 X_api
GPC2 all_cohorts Neuroblastoma Brain - Hypothalamus (N = 202) 1.58 1.45 0.83 X_api
GPC2 all_cohorts Neuroblastoma Brain - Nucleus accumbens (basal ganglia) (N = 246) 1.36 1.28 0.69 X_api
GPC2 all_cohorts Neuroblastoma Brain - Putamen (basal ganglia) (N = 205) 1.32 1.24 0.58 X_api
GPC2 all_cohorts Neuroblastoma Brain - Spinal cord (cervical c-1) (N = 159) 3.34 3.2 1.52 X_api
GPC2 all_cohorts Neuroblastoma Brain - Substantia nigra (N = 139) 1.74 1.59 0.96 X_api
GPC2 all_cohorts Neuroblastoma Breast - Mammary Tissue (N = 459) 2.27 1.88 1.62 X_api
GPC2 all_cohorts Neuroblastoma Cells - Cultured fibroblasts (N = 504) 1.3 1.21 0.6 X_api
GPC2 all_cohorts Neuroblastoma Cells - EBV-transformed lymphocytes (N = 174) 2.61 2.33 1.56 X_api
GPC2 all_cohorts Neuroblastoma Cervix - Ectocervix (N = 9) 4.63 3.68 2.91 X_api
GPC2 all_cohorts Neuroblastoma Cervix - Endocervix (N = 10) 5.14 3.64 4.09 X_api
GPC2 all_cohorts Neuroblastoma Colon - Sigmoid (N = 373) 1.67 1.55 0.83 X_api
GPC2 all_cohorts Neuroblastoma Colon - Transverse (N = 406) 2.02 1.92 0.87 X_api
GPC2 all_cohorts Neuroblastoma Esophagus - Gastroesophageal Junction (N = 375) 1.13 0.99 0.61 X_api
GPC2 all_cohorts Neuroblastoma Esophagus - Mucosa (N = 555) 1.16 1.04 0.59 X_api
GPC2 all_cohorts Neuroblastoma Esophagus - Muscularis (N = 515) 1.19 1.05 0.65 X_api
GPC2 all_cohorts Neuroblastoma Fallopian Tube (N = 9) 3.32 2.8 1.75 X_api
GPC2 all_cohorts Neuroblastoma Heart - Atrial Appendage (N = 429) 0.63 0.56 0.36 X_api
GPC2 all_cohorts Neuroblastoma Heart - Left Ventricle (N = 432) 0.44 0.34 0.42 X_api
GPC2 all_cohorts Neuroblastoma Kidney - Cortex (N = 85) 0.66 0.48 0.75 X_api
GPC2 all_cohorts Neuroblastoma Liver (N = 226) 0.17 0.12 0.2 X_api
GPC2 all_cohorts Neuroblastoma Lung (N = 578) 1.52 1.31 1.01 X_api
GPC2 all_cohorts Neuroblastoma Minor Salivary Gland (N = 162) 2.06 1.84 1.2 X_api
GPC2 all_cohorts Neuroblastoma Muscle - Skeletal (N = 803) 0.45 0.34 0.4 X_api
GPC2 all_cohorts Neuroblastoma Nerve - Tibial (N = 619) 3 2.89 1.11 X_api
GPC2 all_cohorts Neuroblastoma Ovary (N = 180) 5.42 4.51 3.52 X_api
GPC2 all_cohorts Neuroblastoma Pancreas (N = 328) 0.33 0.26 0.32 X_api
GPC2 all_cohorts Neuroblastoma Pituitary (N = 283) 2.24 2.04 1.12 X_api
GPC2 all_cohorts Neuroblastoma Prostate (N = 245) 2.24 2.08 1.05 X_api
GPC2 all_cohorts Neuroblastoma Skin - Not Sun Exposed (Suprapubic) (N = 604) 13.99 13.12 6.07 X_api
GPC2 all_cohorts Neuroblastoma Skin - Sun Exposed (Lower leg) (N = 701) 10.98 10.5 4.54 X_api
GPC2 all_cohorts Neuroblastoma Small Intestine - Terminal Ileum (N = 187) 2.74 2.13 2 X_api
GPC2 all_cohorts Neuroblastoma Spleen (N = 241) 3.1 2.8 1.43 X_api
GPC2 all_cohorts Neuroblastoma Stomach (N = 359) 0.76 0.65 0.46 X_api
GPC2 all_cohorts Neuroblastoma Testis (N = 361) 32.59 32.61 10.03 X_api
GPC2 all_cohorts Neuroblastoma Thyroid (N = 653) 1.07 0.95 0.6 X_api
GPC2 all_cohorts Neuroblastoma Uterus (N = 142) 6.07 4.65 4.41 X_api
GPC2 all_cohorts Neuroblastoma Vagina (N = 156) 3.16 2.98 1.37 X_api
GPC2 all_cohorts Neuroblastoma Whole Blood (N = 755) 1.04 0.8 1.81 X_api
GPC2 all_cohorts Medulloblastoma Medulloblastoma (N = 122) 27.58 23.85 18.41 y_api
GPC2 all_cohorts Medulloblastoma Adipose - Subcutaneous (N = 663) 1.76 1.66 0.82 y_api
GPC2 all_cohorts Medulloblastoma Adipose - Visceral (Omentum) (N = 541) 1.2 1.04 0.65 y_api
GPC2 all_cohorts Medulloblastoma Adrenal Gland (N = 258) 0.72 0.63 0.36 y_api
GPC2 all_cohorts Medulloblastoma Artery - Aorta (N = 432) 1.45 1.3 0.74 y_api
GPC2 all_cohorts Medulloblastoma Artery - Coronary (N = 240) 1.37 1.14 0.95 y_api
GPC2 all_cohorts Medulloblastoma Artery - Tibial (N = 663) 0.75 0.61 0.59 y_api
GPC2 all_cohorts Medulloblastoma Bladder (N = 21) 1.98 1.85 1.25 y_api
GPC2 all_cohorts Medulloblastoma Brain - Amygdala (N = 152) 2.29 2.22 0.86 y_api
GPC2 all_cohorts Medulloblastoma Brain - Anterior cingulate cortex (BA24) (N = 176) 1.86 1.78 0.65 y_api
GPC2 all_cohorts Medulloblastoma Brain - Caudate (basal ganglia) (N = 246) 1.35 1.35 0.5 y_api
GPC2 all_cohorts Medulloblastoma Brain - Cerebellar Hemisphere (N = 215) 3.12 2.79 1.83 y_api
GPC2 all_cohorts Medulloblastoma Brain - Cerebellum (N = 241) 3.27 2.77 1.98 y_api
GPC2 all_cohorts Medulloblastoma Brain - Cortex (N = 255) 1.63 1.53 0.57 y_api
GPC2 all_cohorts Medulloblastoma Brain - Frontal Cortex (BA9) (N = 209) 1.61 1.56 0.59 y_api
GPC2 all_cohorts Medulloblastoma Brain - Hippocampus (N = 197) 2.21 2.09 1 y_api
GPC2 all_cohorts Medulloblastoma Brain - Hypothalamus (N = 202) 1.58 1.45 0.83 y_api
GPC2 all_cohorts Medulloblastoma Brain - Nucleus accumbens (basal ganglia) (N = 246) 1.36 1.28 0.69 y_api
GPC2 all_cohorts Medulloblastoma Brain - Putamen (basal ganglia) (N = 205) 1.32 1.24 0.58 y_api
GPC2 all_cohorts Medulloblastoma Brain - Spinal cord (cervical c-1) (N = 159) 3.34 3.2 1.52 y_api
GPC2 all_cohorts Medulloblastoma Brain - Substantia nigra (N = 139) 1.74 1.59 0.96 y_api
GPC2 all_cohorts Medulloblastoma Breast - Mammary Tissue (N = 459) 2.27 1.88 1.62 y_api
GPC2 all_cohorts Medulloblastoma Cells - Cultured fibroblasts (N = 504) 1.3 1.21 0.6 y_api
GPC2 all_cohorts Medulloblastoma Cells - EBV-transformed lymphocytes (N = 174) 2.61 2.33 1.56 y_api
GPC2 all_cohorts Medulloblastoma Cervix - Ectocervix (N = 9) 4.63 3.68 2.91 y_api
GPC2 all_cohorts Medulloblastoma Cervix - Endocervix (N = 10) 5.14 3.64 4.09 y_api
GPC2 all_cohorts Medulloblastoma Colon - Sigmoid (N = 373) 1.67 1.55 0.83 y_api
GPC2 all_cohorts Medulloblastoma Colon - Transverse (N = 406) 2.02 1.92 0.87 y_api
GPC2 all_cohorts Medulloblastoma Esophagus - Gastroesophageal Junction (N = 375) 1.13 0.99 0.61 y_api
GPC2 all_cohorts Medulloblastoma Esophagus - Mucosa (N = 555) 1.16 1.04 0.59 y_api
GPC2 all_cohorts Medulloblastoma Esophagus - Muscularis (N = 515) 1.19 1.05 0.65 y_api
GPC2 all_cohorts Medulloblastoma Fallopian Tube (N = 9) 3.32 2.8 1.75 y_api
GPC2 all_cohorts Medulloblastoma Heart - Atrial Appendage (N = 429) 0.63 0.56 0.36 y_api
GPC2 all_cohorts Medulloblastoma Heart - Left Ventricle (N = 432) 0.44 0.34 0.42 y_api
GPC2 all_cohorts Medulloblastoma Kidney - Cortex (N = 85) 0.66 0.48 0.75 y_api
GPC2 all_cohorts Medulloblastoma Liver (N = 226) 0.17 0.12 0.2 y_api
GPC2 all_cohorts Medulloblastoma Lung (N = 578) 1.52 1.31 1.01 y_api
GPC2 all_cohorts Medulloblastoma Minor Salivary Gland (N = 162) 2.06 1.84 1.2 y_api
GPC2 all_cohorts Medulloblastoma Muscle - Skeletal (N = 803) 0.45 0.34 0.4 y_api
GPC2 all_cohorts Medulloblastoma Nerve - Tibial (N = 619) 3 2.89 1.11 y_api
GPC2 all_cohorts Medulloblastoma Ovary (N = 180) 5.42 4.51 3.52 y_api
GPC2 all_cohorts Medulloblastoma Pancreas (N = 328) 0.33 0.26 0.32 y_api
GPC2 all_cohorts Medulloblastoma Pituitary (N = 283) 2.24 2.04 1.12 y_api
GPC2 all_cohorts Medulloblastoma Prostate (N = 245) 2.24 2.08 1.05 y_api
GPC2 all_cohorts Medulloblastoma Skin - Not Sun Exposed (Suprapubic) (N = 604) 13.99 13.12 6.07 y_api
GPC2 all_cohorts Medulloblastoma Skin - Sun Exposed (Lower leg) (N = 701) 10.98 10.5 4.54 y_api
GPC2 all_cohorts Medulloblastoma Small Intestine - Terminal Ileum (N = 187) 2.74 2.13 2 y_api
GPC2 all_cohorts Medulloblastoma Spleen (N = 241) 3.1 2.8 1.43 y_api
GPC2 all_cohorts Medulloblastoma Stomach (N = 359) 0.76 0.65 0.46 y_api
GPC2 all_cohorts Medulloblastoma Testis (N = 361) 32.59 32.61 10.03 y_api
GPC2 all_cohorts Medulloblastoma Thyroid (N = 653) 1.07 0.95 0.6 y_api
GPC2 all_cohorts Medulloblastoma Uterus (N = 142) 6.07 4.65 4.41 y_api
GPC2 all_cohorts Medulloblastoma Vagina (N = 156) 3.16 2.98 1.37 y_api
GPC2 all_cohorts Medulloblastoma Whole Blood (N = 755) 1.04 0.8 1.81 y_api

also pasting an excel example for whichever is easier for you. mock_all_cohort_tpm_plot_data.xlsx

where ENSG_id, efo_code, mondo_code, and uberon_code will be added later, after #112 is completed and where plot_api is the api link to each plot

What input data should be used? Which data were used in the version being updated?

gene-expression-rsem-tpm-collapsed.rds 
histologies.tsv

When do you expect the revised analysis will be completed?

this week?

Who will complete the updated analysis?

@komalsrathi

komalsrathi commented 3 years ago

@jharenza is this instead of the metadata.tsv file or instead of individual tsv files corresponding to the plots? If the latter, then should we keep the metadata.tsv file?

jharenza commented 3 years ago

@jharenza is this instead of the metadata.tsv file or instead of individual tsv files corresponding to the plots? If the latter, then should we keep the metadata.tsv file?

This would be instead of all tables - so you would just have two tables at the end, one cohort+cancer_group for all genes and all plots, along with api links and then one cancer_group with cohort being all_cohorts for all genes and all plots with api links. They will somehow enable export of the tables from the long format table (guessing based on api link).

jharenza commented 3 years ago

closing this, as we do not want to implement