diff --git a/.Rbuildignore b/.Rbuildignore index f1b33bd..bf5b863 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -6,3 +6,4 @@ ^docs$ ^pkgdown$ ^\.github$ +CODEOWNERS \ No newline at end of file diff --git a/CODEOWNERS b/CODEOWNERS new file mode 100644 index 0000000..80ea2af --- /dev/null +++ b/CODEOWNERS @@ -0,0 +1 @@ +* @nicolerg \ No newline at end of file diff --git a/DESCRIPTION b/DESCRIPTION index f5de8be..ff35042 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Type: Package Package: MotrpacRatTraining6moData Title: Data for analysis of the MoTrPAC endurance exercise training study in 6-month-old rats -Version: 1.9.1 +Version: 2.0.0 Authors@R: c( person("Nicole", "Gay", , "nicole.r.gay@gmail.com", role = c("cre", "aut")), person("Pierre", "Jean Beltran", , "pjeanbeltran@gmail.com", role = "aut"), diff --git a/NEWS.md b/NEWS.md index 8092abb..5f440bf 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# MotrpacRatTraining6moData 2.0.0 (2023-11-08) + +* Replace all instances of `t65-aorta` with `t99-vena-cava`, and `Aorta` with `Vena Cava`. + # MotrpacRatTraining6moData 1.9.1 (2023-06-02) * Update `MotrpacRatTraining6mo` version requirement. diff --git a/data-raw/OUTLIERS.R b/data-raw/OUTLIERS.R index 2511c8a..cd38395 100644 --- a/data-raw/OUTLIERS.R +++ b/data-raw/OUTLIERS.R @@ -28,13 +28,13 @@ OUTLIERS[assay_code == "immunoassay-rat-mag27plex", assay_code := "immunoassay"] OUTLIERS[,group := gsub(",", "_", group)] # add all 1w, 2w vena cava samples -venacv = data.table(PHENO[PHENO$specimen.processing.sampletypedescription == "Aorta",]) +venacv = data.table(PHENO[PHENO$specimen.processing.sampletypedescription == "Vena Cava",]) table(venacv[,specimen.processing.sampletypedescription]) venacv = venacv[sex == "female" & group %in% c("1w","2w")] venacv[,.(viallabel, sex, group)] out2 = data.table(viallabel = as.character(venacv[,viallabel]), tissue = "VENACV", - tissue_code = "t65-aorta", + tissue_code = "t99-vena-cava", pid = venacv[,pid], group = sprintf("female_%s", venacv[,group]), reason = "BAT contamination") diff --git a/data-raw/outliers.tsv b/data-raw/outliers.tsv index 7452159..e05991a 100644 --- a/data-raw/outliers.tsv +++ b/data-raw/outliers.tsv @@ -21,8 +21,8 @@ viallabel tissue pid group platform reason 90439016105 t61-colon 10486003 male,2w immunoassay-rat-mag27plex large fraction of missing values: 0.7037037 90449016105 t61-colon 10641858 male,2w immunoassay-rat-mag27plex large fraction of missing values: 0.8148148 90292016105 t61-colon 10220917 male,4w immunoassay-rat-mag27plex large fraction of missing values: 0.7037037 -all t65-aorta (vena cava) female,1w all brown adipose contamination -all t65-aorta (vena cava) female,2w all brown adipose contamination +all t99-vena-cava female,1w all brown adipose contamination +all t99-vena-cava female,2w all brown adipose contamination 90406015204 t52-hippocampus,stanford 10306471 female,4w epigen-atac-seq PC1 90423015204 t52-hippocampus,stanford 10424911 male,1w epigen-atac-seq PC1 90217015204 t52-hippocampus,stanford 10023259 male,control epigen-atac-seq PC1 @@ -51,7 +51,7 @@ all t65-aorta (vena cava) female,2w all brown adipose contamination 90571016002 t60-adrenal 10953744 female,1w transcript-rna-seq PC1 90229016102 t61-colon 10026355 male,control transcript-rna-seq PC2 90289016302 t63-testes 10185585 male,4w transcript-rna-seq PC2 -90564016502 t65-aorta 10833331 female,1w transcript-rna-seq PC2 +90564016502 t99-vena-cava 10833331 female,1w transcript-rna-seq PC2 90441016702 t67-small-intestine 10502300 male,2w transcript-rna-seq PC3 90218016803 t68-liver 10024735 male,8w transcript-rna-seq PC2 90266016902 t69-brown-adipose 10046380 female,control transcript-rna-seq PC3 diff --git a/data/METAB_VENACV_DA.rda b/data/METAB_VENACV_DA.rda index 2d7e320..ff93a6d 100644 Binary files a/data/METAB_VENACV_DA.rda and b/data/METAB_VENACV_DA.rda differ diff --git a/data/METAB_VENACV_DA_METAREG.rda b/data/METAB_VENACV_DA_METAREG.rda index 674f5f5..ea336de 100644 Binary files a/data/METAB_VENACV_DA_METAREG.rda and b/data/METAB_VENACV_DA_METAREG.rda differ diff --git a/data/OUTLIERS.rda b/data/OUTLIERS.rda index 1378c54..6cad39c 100644 Binary files a/data/OUTLIERS.rda and b/data/OUTLIERS.rda differ diff --git a/data/PHENO.rda b/data/PHENO.rda index 740beda..2d70763 100644 Binary files a/data/PHENO.rda and b/data/PHENO.rda differ diff --git a/data/TRAINING_REGULATED_FEATURES.rda b/data/TRAINING_REGULATED_FEATURES.rda index d254725..28cd505 100644 Binary files a/data/TRAINING_REGULATED_FEATURES.rda and b/data/TRAINING_REGULATED_FEATURES.rda differ diff --git a/data/TRNSCRPT_VENACV_DA.rda b/data/TRNSCRPT_VENACV_DA.rda index 0e6e523..d4e4368 100644 Binary files a/data/TRNSCRPT_VENACV_DA.rda and b/data/TRNSCRPT_VENACV_DA.rda differ diff --git a/inst/scripts/replace_aorta.R b/inst/scripts/replace_aorta.R new file mode 100644 index 0000000..00b84f9 --- /dev/null +++ b/inst/scripts/replace_aorta.R @@ -0,0 +1,96 @@ +library(data.table) +library(devtools) +load_all() + +# copied from MotrpacRatTraining6mo +list_available_data = function(package=NULL){ + res = utils::data(package=package) + obj = res$results[,3] + # remove objects that can't be called directly + obj = obj[!grepl("\\(", obj)] + return(obj) +} + +# list all available data objects +objs = list_available_data(package="MotrpacRatTraining6moData") + +# identify data objects with "aorta" in them +has_aorta = c() +for (obj in objs){ + print(obj) + # skip ATAC data, which doesn't have vena cava data + if(grepl("ATAC", obj)){ + next() + } + # skip GENE_UNIVERSES, which already uses VENACV + if(obj=="GENE_UNIVERSES"){ + next() + } + + data = get(obj) + if (is.data.frame(data)){ + if (any(data == "t65-aorta", na.rm=TRUE)){ + has_aorta = c(has_aorta, obj) + } + if (any(data == "aorta", na.rm=TRUE)){ + has_aorta = c(has_aorta, obj) + } + if (any(data == "Aorta", na.rm=TRUE)){ + has_aorta = c(has_aorta, obj) + } + }else if (is.vector(data)){ + if("t65-aorta" %in% data){ + has_aorta = c(has_aorta, obj) + } + }else{ + print(sprintf("Not sure what type %s is", obj)) + } +} + +# manually edit data objects +unique(has_aorta) + +data("METAB_VENACV_DA_METAREG") +METAB_VENACV_DA_METAREG$tissue_code[METAB_VENACV_DA_METAREG$tissue_code == "t65-aorta"] = "t99-vena-cava" +stopifnot(!any(METAB_VENACV_DA_METAREG == "t65-aorta", na.rm = TRUE)) +usethis::use_data(METAB_VENACV_DA_METAREG, overwrite = T) + +data("METAB_VENACV_DA") +METAB_VENACV_DA$tissue_code[METAB_VENACV_DA$tissue_code == "t65-aorta"] = "t99-vena-cava" +stopifnot(!any(METAB_VENACV_DA == "t65-aorta", na.rm = TRUE)) +usethis::use_data(METAB_VENACV_DA, overwrite = T) + +data("OUTLIERS") +OUTLIERS$tissue_code[OUTLIERS$tissue_code == "t65-aorta"] = "t99-vena-cava" +stopifnot(!any(OUTLIERS == "t65-aorta", na.rm = TRUE)) +usethis::use_data(OUTLIERS, overwrite = T) + +data("TISSUE_ABBREV_TO_CODE") +TISSUE_ABBREV_TO_CODE[TISSUE_ABBREV_TO_CODE == "t65-aorta"] = "t99-vena-cava" +stopifnot(!any(TISSUE_ABBREV_TO_CODE == "t65-aorta", na.rm = TRUE)) +usethis::use_data(TISSUE_ABBREV_TO_CODE, overwrite = T) + +data("TISSUE_CODE_TO_ABBREV") +names(TISSUE_CODE_TO_ABBREV)[names(TISSUE_CODE_TO_ABBREV) == "t65-aorta"] = "t99-vena-cava" +stopifnot(!any(TISSUE_CODE_TO_ABBREV == "t65-aorta", na.rm = TRUE)) +stopifnot(!any(names(TISSUE_CODE_TO_ABBREV) == "t65-aorta", na.rm = TRUE)) +usethis::use_data(TISSUE_CODE_TO_ABBREV, overwrite = T) + +data("TRAINING_REGULATED_FEATURES") +TRAINING_REGULATED_FEATURES$tissue_code[TRAINING_REGULATED_FEATURES$tissue_code == "t65-aorta"] = "t99-vena-cava" +stopifnot(!any(TRAINING_REGULATED_FEATURES == "t65-aorta", na.rm = TRUE)) +usethis::use_data(TRAINING_REGULATED_FEATURES, overwrite = T) + +data("TRNSCRPT_VENACV_DA") +TRNSCRPT_VENACV_DA$tissue_code[TRNSCRPT_VENACV_DA$tissue_code == "t65-aorta"] = "t99-vena-cava" +stopifnot(!any(TRNSCRPT_VENACV_DA == "t65-aorta", na.rm = TRUE)) +usethis::use_data(TRNSCRPT_VENACV_DA, overwrite = T) + +data("PHENO") +PHENO[PHENO$tissue_code_no == "T65",] +PHENO$tissue_code_no[PHENO$tissue_code_no == "T65"] = "T99" +PHENO$tissue_description[PHENO$tissue_description == "Aorta"] = "Vena Cava" +PHENO$specimen.processing.aliquotdescription = gsub("Aorta", "Vena Cava", PHENO$specimen.processing.aliquotdescription) +PHENO$specimen.processing.sampletypedescription[PHENO$specimen.processing.sampletypedescription == "Aorta"] = "Vena Cava" +stopifnot(!any(PHENO == "t65-aorta", na.rm = TRUE)) +usethis::use_data(PHENO, overwrite = T) diff --git a/inst/scripts/save_sample_level_data_metabolomics.Rmd b/inst/scripts/save_sample_level_data_metabolomics.Rmd index 143f9a8..8a494ec 100644 --- a/inst/scripts/save_sample_level_data_metabolomics.Rmd +++ b/inst/scripts/save_sample_level_data_metabolomics.Rmd @@ -339,7 +339,7 @@ separate(dataset,into=c("phase","tissue","ome","modality","platform"), #5. Remove vena cava contaminated samples--------------------------------------- # First remove female 1w and 2w vena cava samples from data mutate(data_for_dea = pmap(list(tissue,data_for_dea,pheno), function(tissue,dat,pheno){ - if(tissue == "t65-aorta"){ + if(tissue == "t99-vena-cava"){ to_include <- pheno %>% filter(!((sex == "F") & (tr_group == "1_0" | tr_group == "2_0"))) return(dat[,to_include$viallabel]) diff --git a/vignettes/MotrpacRatTraining6moData.Rmd b/vignettes/MotrpacRatTraining6moData.Rmd index fdcc9d9..6446433 100644 --- a/vignettes/MotrpacRatTraining6moData.Rmd +++ b/vignettes/MotrpacRatTraining6moData.Rmd @@ -64,7 +64,7 @@ div.yellow {
-This vignette is under construction. If something is unclear or obviously missing, +If you run into problems, please submit an issue [here](https://github.com/MoTrPAC/MotrpacRatTraining6moData/issues).