Merge pull request #158 from bhklab/156-warning-on-bioc

156 warning on bioc

.github/workflows/R-CMD-check-bioc.yml

@@ -22,10 +22,6 @@
 
 on:
   push:
-    branches:
-      - master
-      - main
-      - devel
   pull_request:
     branches:
       - master

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PharmacoGx
 Type: Package
 Title: Analysis of Large-Scale Pharmacogenomic Data
-Version: 3.7.3
+Version: 3.7.5
 Date: 2024-04-08
 Authors@R: c(
     person(given="Petr", family="Smirnov", email="[email protected]",

NAMESPACE

@@ -111,8 +111,6 @@ importClassesFrom(CoreGx,CoreSet)
 importClassesFrom(CoreGx,LongTable)
 importClassesFrom(CoreGx,TreatmentResponseExperiment)
 importClassesFrom(MultiAssayExperiment,MultiAssayExperiment)
-importClassesFrom(S4Vectors,DataFrame)
-importClassesFrom(S4Vectors,List)
 importFrom(Biobase,AnnotatedDataFrame)
 importFrom(BiocParallel,bplapply)
 importFrom(CoreGx,"sampleInfo<-")
@@ -145,7 +143,6 @@ importFrom(CoreGx,sampleNames)
 importFrom(CoreGx,subsetByFeature)
 importFrom(CoreGx,treatmentNames)
 importFrom(CoreGx,updateSampleId)
-importFrom(MultiAssayExperiment,MultiAssayExperiment)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,SimpleList)
 importFrom(S4Vectors,metadata)
@@ -162,22 +159,11 @@ importFrom(SummarizedExperiment,colData)
 importFrom(SummarizedExperiment,rowData)
 importFrom(boot,boot)
 importFrom(boot,boot.ci)
-importFrom(checkmate,assert)
-importFrom(checkmate,assertCharacter)
-importFrom(checkmate,assertClass)
-importFrom(checkmate,assertDataFrame)
 importFrom(checkmate,assertDataTable)
 importFrom(checkmate,assertInt)
-importFrom(checkmate,assertList)
 importFrom(checkmate,assertLogical)
 importFrom(checkmate,assertNumeric)
-importFrom(checkmate,assertSubset)
 importFrom(coop,pcor)
-importFrom(data.table,":=")
-importFrom(data.table,as.data.table)
-importFrom(data.table,data.table)
-importFrom(data.table,merge.data.table)
-importFrom(data.table,tstrsplit)
 importFrom(downloader,download)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,palette)
@@ -225,8 +211,6 @@ importFrom(utils,sessionInfo)
 importFrom(utils,setTxtProgressBar)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.table)
-importMethodsFrom(BiocGenerics,"annotation<-")
-importMethodsFrom(BiocGenerics,annotation)
 importMethodsFrom(CoreGx,"annotation<-")
 importMethodsFrom(CoreGx,"curation<-")
 importMethodsFrom(CoreGx,"datasetType<-")

R/PharmacoSet-class.R

@@ -341,130 +341,6 @@ checkPsetStructure <-
       }
     }
 
-#    #####
-#    # Checking cell
-#    #####
-#    if('tissueid' %in% colnames(sampleInfo(object))) {
-#      if('unique.tissueid' %in% colnames(curation(object)$tissue))
-#      {
-#        if(length(intersect(rownames(curation(object)$tissue),
-#                            sampleNames(object)) != nrow(sampleInfo(object))) {
-#          message('rownames of curation tissue slot should be the same as cell
-#                  slot (curated cell ids)')
-#        } else{
-#          if(length(intersect(sampleInfo(object)$tissueid,
-#                              curation(object)$tissue$unique.tissueid)) !=
-#             length(table(sampleInfo(object)$tissueid))){
-#            message('tissueid should be the same as unique tissue id from tissue
-#                    curation slot')
-#          }
-#        }
-#      } else {
-#        message('unique.tissueid which is curated tissue id across data set
-#                should be a column of tissue curation slot')
-#      }
-#      if(any(is.na(sampleInfo(object)[,'tissueid']) | sampleInfo(object)[,'tissueid']=='',
-#             na.rm=TRUE)){
-#        message(sprintf('There is no tissue type for this cell line(s): %s',
-#                        paste(rownames(sampleInfo(object))[which(is.na(
-#                          sampleInfo(object)[,'tissueid']) |
-#                            sampleInfo(object)[,'tissueid']=='')], collapse=' ')))
-#      }
-#    } else {
-#      warning('tissueid does not exist in cell slot')
-#    }
-#
-#    if('unique.sampleid' %in% colnames(curation(object)$cell)) {
-#      if(length(intersect(curation(object)$cell$unique.sampleid,
-#                          sampleNames(object)) != nrow(sampleInfo(object))) {
-#        print('rownames of cell slot should be curated cell ids')
-#      }
-#    } else {
-#      print('unique.sampleid which is curated cell id across data set should be a
-#            column of cell curation slot')
-#    }
-##     if("sampleid" %in% colnames(sampleInfo(object))) {
-##       if(length(intersect(curation(object)$cell$sampleid, sampleNames(object))
-##    != nrow(sampleInfo(object))) {
-##         print('values of sampleid column should be curated cell line ids')
-##       }
-##     } else {
-##       print('sampleid which is curated cell id across data set should be a column of cell slot')
-##     }
-#
-#    if(length(intersect(rownames(curation(object)$cell),
-#                        sampleNames(object)) != nrow(sampleInfo(object))) {
-#      print('rownames of curation cell slot should be the same as cell slot
-#            (curated cell ids)')
-#    }
-#
-#    if('unique.treatmentid' %in% colnames(curation(object)$treatment)) {
-#      if(length(intersect(curation(object)$treatment$unique.treatmentid,
-#                          rownames(treatmentInfo(drug)))) != nrow(treatmentInfo(drug))) {
-#        print('rownames of drug slot should be curated drug ids')
-#      }
-#    } else {
-#      print('unique.treatmentid which is curated drug id across data set should be a
-#            column of drug curation slot')
-#    }
-#
-##     if("treatmentid" %in% colnames(treatmentInfo(drug))) {
-##       if(length(intersect(curation(object)$treatment$treatmentid,
-##    rownames(treatmentInfo(drug)))) != nrow(treatmentInfo(drug))) {
-##         print('values of treatmentid column should be curated drug ids')
-##       }
-##     } else {
-##       print('treatmentid which is curated drug id across data set should be a
-##    column of drug slot')
-##     }
-#
-#    if(length(intersect(rownames(curation(object)$cell),
-#                        sampleNames(object)) != nrow(sampleInfo(object))) {
-#      print('rownames of curation drug slot should be the same as drug
-#            slot (curated drug ids)')
-#    }
-#
-#    if(!is(sampleInfo(object), 'data.frame')) {
-#      warning('cell slot class type should be dataframe')
-#    }
-#    if(!is(treatmentInfo(drug), 'data.frame')) {
-#      warning('drug slot class type should be dataframe')
-#    }
-#    if(datasetType(object) %in% c('sensitivity', 'both'))
-#    {
-#      if(!is(sensitivityInfo(object), 'data.frame')) {
-#        warning('sensitivity info slot class type should be dataframe')
-#      }
-#      if("sampleid" %in% colnames(sensitivityInfo(object))) {
-#        if(!all(sensitivityInfo(object)[,"sampleid"] %in% sampleNames(object)){
-#          warning('not all the cell lines in sensitivity data are in cell slot')
-#        }
-#      }else {
-#        warning('sampleid does not exist in sensitivity info')
-#      }
-#      if("treatmentid" %in% colnames(sensitivityInfo(object))) {
-#        drug.ids <- unique(sensitivityInfo(object)[,"treatmentid"])
-#        drug.ids <- drug.ids[grep('///',drug.ids, invert=TRUE)]
-#        if(!all(drug.ids %in% rownames(treatmentInfo(drug)))) {
-#          print('not all the drugs in sensitivity data are in drug slot')
-#        }
-#      }else {
-#        warning('treatmentid does not exist in sensitivity info')
-#      }
-#
-#      if(any(!is.na(sensitivityRaw(object)))) {
-#        if(!all(dimnames(sensitivityRaw(object))[[1]] %in%
-#                rownames(sensitivityInfo(object)))) {
-#          warning('For some experiments there is raw sensitivity data but no
-#                  experiment information in sensitivity info')
-#        }
-#      }
-#      if(!all(rownames(sensitivityProfiles(object)) %in%
-#              rownames(sensitivityInfo(object)))) {
-#        warning('For some experiments there is sensitivity profiles but no
-#                experiment information in sensitivity info')
-#      }
-#    }
 }
 
 

R/methods-[.R

@@ -1,6 +1,4 @@
 # ==== PharmacoSet Class
-
-
 #'`[`
 #'
 #' @examples

R/methods-summarizeSensitivityProfiles.R

@@ -26,10 +26,18 @@
 #' @importMethodsFrom CoreGx summarizeSensitivityProfiles
 #' @export
 setMethod("summarizeSensitivityProfiles", signature(object="PharmacoSet"),
-    function(object, sensitivity.measure="auc_recomputed", cell.lines, profiles_assay = "profiles",
-    treatment_col = "treatmentid", sample_col = "sampleid",
-    drugs, summary.stat=c("mean", "median", "first", "last", "max", "min"),
-    fill.missing=TRUE, verbose=TRUE) {
+    function(
+      object, 
+      sensitivity.measure="auc_recomputed", 
+      cell.lines, 
+      profiles_assay = "profiles",
+      treatment_col = "treatmentid", 
+      sample_col = "sampleid",
+      drugs, 
+      summary.stat=c("mean", "median", "first", "last", "max", "min"),
+      fill.missing=TRUE, 
+      verbose=TRUE
+  ) {
   if (is(treatmentResponse(object), 'LongTable'))
     .summarizeSensProfiles(object, sensitivity.measure, profiles_assay = profiles_assay,
       treatment_col, sample_col, cell.lines, drugs, summary.stat, fill.missing)
@@ -177,16 +185,6 @@ setMethod("summarizeSensitivityProfiles", signature(object="PharmacoSet"),
   rownames(result) <- drugs
   colnames(result) <- cell.lines
 
-  # if(verbose){
-
-  #   message(sprintf("Summarizing %s sensitivity data for:\t%s", sensitivity.measure, annotation(object)$name))
-  #   total <- length(drugs)*length(cell.lines)
-  #   # create progress bar
-  #   pb <- utils::txtProgressBar(min=0, max=total, style=3)
-  #   i <- 1
-
-
-  # }
   if(is.factor(dd[, sensitivity.measure]) | is.character(dd[, sensitivity.measure])){
     warning("Sensitivity measure is stored as a factor or character in the pSet. This is incorrect.\n
              Please correct this and/or file an issue. Fixing in the call of this function.")
@@ -213,9 +211,6 @@ setMethod("summarizeSensitivityProfiles", signature(object="PharmacoSet"),
   pp_dd <- pp_dd[pp_dd[,"sampleid"] %in% cell.lines & pp_dd[,"treatmentid"]%in%drugs,]
 
   tt <- reshape2::acast(pp_dd, treatmentid ~ sampleid, fun.aggregate=summary.function, value.var="sensitivity.measure")
- # tt <- tt[drugs, cell.lines]
-
-
 
   result[rownames(tt), colnames(tt)] <- tt
 

R/updateObject-methods.R

@@ -3,7 +3,11 @@
 #' @param object A `PharmacoSet` object to update the class structure for.
 #'
 #' @return `PharmacoSet` with update class structure.
-#'
+#' 
+#' @examples
+#' data(GDSCsmall)
+#' updateObject(GDSCsmall)
+#' 
 #' @md
 #' @importMethodsFrom CoreGx updateObject
 #' @export