In sgosline/mpnstXenoModeling: MPNST Xenograft Modeling

knitr::opts_chunk$set(echo = FALSE)
require(mpnstXenoModeling)

Trouble making a Xeva object

I'm having trouble getting a Xeva object and the errors are non-informative. Below documents my efforts. We first just get the data and load it into a format that we can read.

  loadPDXData()
  require(dplyr)
  drugDat = #subset(drugData,individualID==specimenId)%>%
    drugData%>%
    dplyr::select(model.id,patient.id='individualID',drug,volume,time)%>%
   # dplyr::mutate(model.id=as.character(model.id))%>%
    dplyr::mutate(model.id=stringr::str_replace(model.id,'_[0-9]',''))%>%
    rowwise()%>%
    mutate(batch=paste(patient.id,drug))%>%ungroup()%>%
    mutate(volume=as.numeric(volume))%>%
    subset(!is.na(volume))

  head(drugDat)

We first separate out vehicle vs. control, so we can create a batch for each PDX/drug combination. here is our experimental design.

  drugD = subset(drugDat,drug!='vehicle')
  contD = subset(drugDat,drug=='vehicle')

  expDesign =lapply(unique(drugD$batch),function(x){
      pat_drug=unlist(strsplit(x,split=' '))
      treats = subset(drugD,batch==x)%>%
          select(model.id)%>%
          unique()
      conts = subset(contD,patient.id==pat_drug[1])%>%
        select(model.id)%>%
          unique()

      list(batch.name=x,
            treatment=as.character(treats$model.id),
            control=as.character(conts$model.id))})
  print(expDesign)

Now we can create a model-patient mapping.

  model=drugDat%>%dplyr::select(model.id,patient.id)%>%
      distinct()%>%
      dplyr::mutate(tissue='MPNST')%>%
      dplyr::mutate(tissue.name='Malignant Peripheral Nerve Sheath Tumor')%>%
      ungroup()
  head(model)

Next we have the experiment data.

  experiment=rbind(drugD,contD)%>%
      mutate()%>%
    dplyr::select(-c(batch,patient.id))

  head(experiment)

Next up we format the drug table and the gene expression object.

  drug = dplyr::select(experiment,drug)%>%distinct()%>%
    dplyr::mutate(treatment.type='single')%>%
    dplyr::rename(drug.id='drug')%>%
    dplyr::mutate(standard.name=drug.id)%>%
    dplyr::mutate(treatment.target='None')
  head(drug)

  rnaDat = rnaSeq%>%distinct()%>%
    tidiedTableToExpressionSet()
  print(rnaDat)

Lastly we get the modToBiobaseMap:

  modToBiobaseMap = drugDat%>%select(model.id,biobase.id='patient.id')%>%
      distinct()%>%
      mutate(mDataType='RNASeq')
  #data.frame(model.id=c(unique(experiment$model.id),unique(cont$model.id)),
  #                             biobase.id=c(unique(experiment$patient.id),unique(cont$patient.id)))
  #modToBiobaseMap$mDataType='RNASeq'
  head(modToBiobaseMap)

So I have all the data! Woohoo! And it has worked if I only put one sample in each object. However, when I put all the samples in it barfs:

# try(xeva.set<- Xeva::createXevaSet(name="MPNST PDX Data", 
#                           model=as.data.frame(model), drug=as.data.frame(drug),
#                           experiment=as.data.frame(experiment), expDesign=expDesign,
#                           molecularProfiles=list(RNASeq = rnaDat),
#                           modToBiobaseMap = as.data.frame(modToBiobaseMap)))

sgosline/mpnstXenoModeling documentation built on Dec. 10, 2022, 8:33 a.m.