Fixed warning message

crisprVerse · Oct 12, 2022 · d03c775 · d03c775
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Showing 3 changed files with 16 additions and 25 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: crisprScoreData
-Version: 1.1.3
-Date: 2022-06-16
+Version: 1.1.4
+Date: 2022-10-12
 Title: Pre-trained models for the crisprScore package
 Authors@R: c(
     person("Jean-Philippe", "Fortin", email = "fortin946@gmail.com", role = c("aut", "cre", "cph")))

diff --git a/inst/extdata/metadata.csv b/inst/extdata/metadata.csv
@@ -1,13 +1,10 @@
-"Title","Description","BiocVersion","Genome","SourceType","SourceUrl","SourceVersion","Species","TaxonomyId","Coordinate_1_based","DataProvider","Maintainer","RDataClass","DispatchClass","RDataPath"
-"DeepWt.hdf5","DeepHF pretrained model for widtype Cas9.","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/DeepHF/DeepWt.hdf5"
-"DeepWt_T7.hdf5","DeepHF pretrained model for widtype Cas9 (T7 promoter).","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/DeepHF/DeepWt_T7.hdf5"
-"DeepWt_U6.hdf5","DeepHF pretrained model for widtype Cas9 (U6 promoter).","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/DeepHF/DeepWt_U6.hdf5"
-"esp_rnn_model.hdf5","DeepHF pretrained model for EspCas9.","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/DeepHF/esp_rnn_model.hdf5"
-"hf_rnn_model.hdf5","DeepHF pretrained model for HFCas9.","3.14",NA,"HDF5","https://github.com/izhangcd/DeepHF","1",NA,NA,TRUE,"Fudan University","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/DeepHF/hf_rnn_model.hdf5"
-"Model_weights.pkl","Lindel pretrained model weights.","3.14",NA,"TXT","https://github.com/shendurelab/Lindel","1",NA,NA,TRUE,"University of Washington","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/Lindel/Model_weights.pkl"
-"CRISPRa_model.pkl","Weissman pretrained model for CRISPRa.","3.14",NA,"TXT","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/Weissman/CRISPRa_model.pkl"
-"CRISPRi_model.pkl","Weissman pretrained model for CRISPRi.","3.14",NA,"TXT","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/Weissman/CRISPRi_model.pkl"
-"crispria_dnase_human_K562_hg38.bigWig","Processed DNase-seq data for K562 lifted to hg38","3.14",NA,"BigWig","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/Weissman/crispria_dnase_human_K562_hg38.bigWig"
-"crispria_faire_human_K562_hg38.bigWig","Processed FAIRE-seq data for K562 lifted to hg38","3.14",NA,"BigWig","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/Weissman/crispria_faire_human_K562_hg38.bigWig"
-"crispria_mnase_human_K562_hg38.bigWig","Processed MNase-seq data for K562 lifted to hg38","3.14",NA,"BigWig","https://github.com/mhorlbeck/CRISPRiaDesign","1",NA,NA,TRUE,"UCSF","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/Weissman/crispria_mnase_human_K562_hg38.bigWig"
-"RFcombined.rds","CasRx-RF pretrained random forest model for CasRx.","3.14",NA,"RDS","https://gitlab.com/sanjanalab/cas13/","1",NA,NA,TRUE,"New York Genome Center","Jean-Philippe Fortin <fortin946@gmail.com>","character","FilePath","crisprScoreData/CasRxRF/RFcombined.rds"
+Title,Description,BiocVersion,Genome,SourceType,SourceUrl,SourceVersion,Species,TaxonomyId,Coordinate_1_based,DataProvider,Maintainer,RDataClass,DispatchClass,RDataPath
+DeepWt.hdf5,DeepHF pretrained model for widtype Cas9.,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/DeepHF/DeepWt.hdf5
+DeepWt_T7.hdf5,DeepHF pretrained model for widtype Cas9 (T7 promoter).,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/DeepHF/DeepWt_T7.hdf5
+DeepWt_U6.hdf5,DeepHF pretrained model for widtype Cas9 (U6 promoter).,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/DeepHF/DeepWt_U6.hdf5
+esp_rnn_model.hdf5,DeepHF pretrained model for EspCas9.,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/DeepHF/esp_rnn_model.hdf5
+hf_rnn_model.hdf5,DeepHF pretrained model for HFCas9.,3.14,NA,HDF5,https://github.com/izhangcd/DeepHF,1,NA,NA,TRUE,Fudan University,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/DeepHF/hf_rnn_model.hdf5
+Model_weights.pkl,Lindel pretrained model weights.,3.14,NA,TXT,https://github.com/shendurelab/Lindel,1,NA,NA,TRUE,University of Washington,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/Lindel/Model_weights.pkl
+CRISPRa_model.pkl,Weissman pretrained model for CRISPRa.,3.14,NA,TXT,https://github.com/mhorlbeck/CRISPRiaDesign,1,NA,NA,TRUE,UCSF,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/Weissman/CRISPRa_model.pkl
+CRISPRi_model.pkl,Weissman pretrained model for CRISPRi.,3.14,NA,TXT,https://github.com/mhorlbeck/CRISPRiaDesign,1,NA,NA,TRUE,UCSF,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/Weissman/CRISPRi_model.pkl
+RFcombined.rds,CasRx-RF pretrained random forest model for CasRx.,3.14,NA,RDS,https://gitlab.com/sanjanalab/cas13/,1,NA,NA,TRUE,New York Genome Center,Jean-Philippe Fortin <fortin946@gmail.com>,character,FilePath,crisprScoreData/CasRxRF/RFcombined.rds
diff --git a/inst/scripts/make-metadata.R b/inst/scripts/make-metadata.R
@@ -7,9 +7,6 @@ files <- c("DeepWt.hdf5",
            "Model_weights.pkl",
            "CRISPRa_model.pkl",
            "CRISPRi_model.pkl",
-           "crispria_dnase_human_K562_hg38.bigWig",
-           "crispria_faire_human_K562_hg38.bigWig",
-           "crispria_mnase_human_K562_hg38.bigWig",
            "RFcombined.rds")
 nfiles <- length(files)
 sources <- gsub("\\.","",str_extract(files, "\\.+.*"))
@@ -22,7 +19,7 @@ url_weissman <- "https://github.com/mhorlbeck/CRISPRiaDesign"
 url_casrxrf  <- "https://gitlab.com/sanjanalab/cas13/"
 urls <- c(rep(url_deephf,5),
           url_lindel,
-          rep(url_weissman,5),
+          rep(url_weissman,2),
           url_casrxrf)
 dess <- c("DeepHF pretrained model for widtype Cas9.",
           "DeepHF pretrained model for widtype Cas9 (T7 promoter).",
@@ -32,19 +29,16 @@ dess <- c("DeepHF pretrained model for widtype Cas9.",
           "Lindel pretrained model weights.",
           "Weissman pretrained model for CRISPRa.",
           "Weissman pretrained model for CRISPRi.",
-          "Processed DNase-seq data for K562 lifted to hg38",
-          "Processed FAIRE-seq data for K562 lifted to hg38",
-          "Processed MNase-seq data for K562 lifted to hg38",
           "CasRx-RF pretrained random forest model for CasRx.")
 titles <- files
 providers <- c(rep("Fudan University", 5),
                "University of Washington",
-               rep("UCSF", 5),
+               rep("UCSF", 2),
                "New York Genome Center")
 paths1 <- paste0("crisprScoreData/DeepHF/", files[1:5])
 paths2 <- paste0("crisprScoreData/Lindel/", files[6])
-paths3 <- paste0("crisprScoreData/Weissman/", files[7:11])
-paths4 <- paste0("crisprScoreData/CasRxRF/", files[12])
+paths3 <- paste0("crisprScoreData/Weissman/", files[7:9])
+paths4 <- paste0("crisprScoreData/CasRxRF/", files[10])
 paths  <- c(paths1, paths2, paths3, paths4)
 
 metadata <- data.frame(Title=titles,