add csv for tables s2 and s3

UCSC-Treehouse · Aug 27, 2020 · 73d4d28 · 73d4d28
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commit 73d4d28
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Showing 13 changed files with 84 additions and 5 deletions.
diff --git a/results/Figure_1.pdf b/results/Figure_1.pdf
diff --git a/results/Figure_1.png b/results/Figure_1.png
diff --git a/results/Figure_2.pdf b/results/Figure_2.pdf
diff --git a/results/Figure_2.png b/results/Figure_2.png
diff --git a/results/Figure_3.pdf b/results/Figure_3.pdf
diff --git a/results/Figure_3.png b/results/Figure_3.png
diff --git a/results/Figure_S1.pdf b/results/Figure_S1.pdf
diff --git a/results/Figure_S2.pdf b/results/Figure_S2.pdf
diff --git a/results/Table_S2_repo_table.csv b/results/Table_S2_repo_table.csv
@@ -0,0 +1,6 @@
+Name,Abbreviation,URL
+Short Read Archive,SRA,https://www.ncbi.nlm.nih.gov/sra
+European Genome-phenome Archive,EGA,https://www.ebi.ac.uk/ega/home
+St. Jude Cloud,SJC,https://www.stjude.cloud/
+Database of Genotypes and Phenotypes,dbGaP,https://www.ncbi.nlm.nih.gov/gap/
+Cavatica,Cavatica,https://cavatica.squarespace.com/
diff --git a/results/Table_S3_cohort_table.csv b/results/Table_S3_cohort_table.csv
@@ -0,0 +1,49 @@
+Cohort code,Cohort name,Source repository,Repository cohort accession,N in cohort
+Cohort_1,TARGET-10,dbGaP,phs000218,337
+Cohort_2,SJC_BALL,SJC,SJC-DS-1001,141
+Cohort_3,TARGET-20,dbGaP,phs000218,137
+Cohort_4,EGAD00001003279,EGA,EGAD00001003279,127
+Cohort_5,SJC_AMLM,SJC,SJC-DS-1001,103
+Cohort_6,phs000673,dbGaP,phs000673,89
+Cohort_7,TARGET-40,dbGaP,phs000218,88
+Cohort_8,phs000720,dbGaP,phs000720,84
+Cohort_9,SJC_HGG,SJC,SJC-DS-1001,82
+Cohort_10,SJC_EPD,SJC,SJC-DS-1001,78
+Cohort_11,TARGET-52,dbGaP,phs000218,65
+Cohort_12,EGAD00001001098,EGA,EGAD00001001098,63
+Cohort_13,phs000768,dbGaP,phs000768,62
+Cohort_14,SJC_ETV,SJC,SJC-DS-1001,56
+Cohort_15,SJC_LGG,SJC,SJC-DS-1001,54
+Cohort_16,SJC_CBF,SJC,SJC-DS-1001,44
+Cohort_17,SJC_RHB,SJC,SJC-DS-1001,43
+Cohort_18,EGAD00001001620,EGA,EGAD00001001620,39
+Cohort_19,phs000699,dbGaP,phs000699,35
+Cohort_20,CBTTC,Cavatica,CBTTC,31
+Cohort_21,SJC_ERG,SJC,SJC-DS-1001,31
+Cohort_22,SJC_PHALL,SJC,SJC-DS-1001,26
+Cohort_23,EGAD00001001666,EGA,EGAD00001001666,25
+Cohort_24,SJC_CPC,SJC,SJC-DS-1001,25
+Cohort_26,phs000900,dbGaP,phs000900,24
+Cohort_25,EGAD00001000648,EGA,EGAD00001000648,24
+Cohort_30,TARGET-21,dbGaP,phs000218,23
+Cohort_27,EGAD00001000356,EGA,EGAD00001000356,23
+Cohort_28,EGAD00001000617,EGA,EGAD00001000617,23
+Cohort_29,SJC_OS,SJC,SJC-DS-1001,23
+Cohort_31,EGAD00001001927,EGA,EGAD00001001927,22
+Cohort_32,EGAD00001002680,EGA,EGAD00001002680,19
+Cohort_33,SRP126664,SRA,SRP126664,19
+Cohort_34,EGAD00001000158,EGA,EGAD00001000158,17
+Cohort_35,SRP092501,SRA,SRP092501,15
+Cohort_36,EGAD00001000826,EGA,EGAD00001000826,10
+Cohort_37,SJC_E,SJC,SJC-DS-1001,8
+Cohort_38,SJC_MB,SJC,SJC-DS-1001,8
+Cohort_41,TARGET-30,dbGaP,phs000218,7
+Cohort_39,SJC_HYPO,SJC,SJC-DS-1001,7
+Cohort_40,SJC_MEL,SJC,SJC-DS-1001,7
+Cohort_42,EGAD00001000328,EGA,EGAD00001000328,6
+Cohort_44,SJC_Other,SJC,SJC-DS-1001,6
+Cohort_43,SJC_INF,SJC,SJC-DS-1001,6
+Cohort_45,SJC_WLM,SJC,SJC-DS-1001,6
+Cohort_47,TARGET-50,dbGaP,phs000218,4
+Cohort_46,SRP006575,SRA,SRP006575,4
+Cohort_48,SRP040454,SRA,SRP040454,3
diff --git a/results/disease_freq_table.csv b/results/disease_freq_table.csv
@@ -0,0 +1,18 @@
+Disease,n,percent
+Acute lymphoblastic leukemia,680,31.2%
+Acute myeloid leukemia,221,10.1%
+Medulloblastoma,201,9.2%
+Glioma,193,8.9%
+Osteosarcoma,157,7.2%
+Acute megakaryoblastic leukemia,103,4.7%
+Ependymoma,98,4.5%
+Ewing sarcoma,70,3.2%
+Rhabdoid tumor,65,3.0%
+Rhabdomyosarcoma,53,2.4%
+Lymphoma,49,2.2%
+Embryonal rhabdomyosarcoma,42,1.9%
+Alveolar rhabdomyosarcoma,40,1.8%
+Glioblastoma multiforme,29,1.3%
+Choroid plexus carcinoma,25,1.1%
+Synovial sarcoma,22,1.0%
+Other,131,6.0%
diff --git a/rna-seq-survey-MS-v20.Rmd b/rna-seq-survey-MS-v20.Rmd
@@ -172,6 +172,7 @@ disease_freq_table <- counts_and_meta$disease %>%
 colnames(disease_freq_table)[1]="Disease"
 
 write_tsv(disease_freq_table, "results/disease_freq_table.tsv")
+write_csv(disease_freq_table, "results/disease_freq_table.csv")
 
 disease_freq_table  %>%
   kable %>% 
@@ -249,6 +250,7 @@ repo_table <- repo_info %>%
   select(-source_accession_pattern) 
 
 write_tsv(repo_table, "results/Table_S2_repo_table.tsv")
+write_csv(repo_table, "results/Table_S2_repo_table.csv")
 
 repo_table %>%
   kable %>% 
@@ -267,6 +269,7 @@ cohort_table <- counts_and_meta %>%
 colnames(cohort_table) <- to_any_case(colnames(cohort_table), case = "sentence")
 
 write_tsv(cohort_table, "results/Table_S3_cohort_table.tsv")
+write_csv(cohort_table, "results/Table_S3_cohort_table.csv")
 
 
 

diff --git a/rna-seq-survey-MS-v20.html b/rna-seq-survey-MS-v20.html