{"Package":"imcExperiment","Title":"Mass Cytometry S4 Class Structure Pipeline for Images","Version":"0.99.0","Authors@R":"person(\"Anthony\", \"Colombo\", email = \"anthonycolombo60@gmail.com\", role=c(\"aut\",\"cre\"))","Maintainer":"Anthony Colombo ","Description":"Containerizes cytometry data and allows for S4 class structure to extend slots related to cell morphology, spatial coordinates, phenotype network information, and unique cellular labeling.","Depends":"R (>= 4.0), SingleCellExperiment, methods","Imports":"SummarizedExperiment, S4Vectors, spatstat.geom, stats","Suggests":"knitr, rmarkdown","License":"MIT + file LICENSE","biocViews":"Software, WorkflowStep, MultipleComparison","Encoding":"UTF-8","RoxygenNote":"7.1.1","VignetteBuilder":"knitr","NeedsCompilation":"no","Packaged":"2021-08-18 17:33:19 UTC; UOSC","Author":"Anthony Colombo [aut, cre]","Repository":"CRAN","Date/Publication":"2021-08-19 09:20:02 UTC","repoType":"cran","tarballUrl":"ftp://cran.r-project.org/pub/R/src/contrib/imcExperiment_0.99.0.tar.gz","jsonAuthors":[{"name":"Anthony Colombo","email":"anthonycolombo60@gmail.com","maintainer":true}],"readme":"# imcExperiment data container\nContainerizing IMC data into the SummarizedExperiment class, this container inherits packages from FlowSOM and diffcyt to compute clusters and test for differential abundance or state heterogeneity.\n Creating a flowSet is cumbersome, so we can stream-line into a summarized experiment into a quick and fast way to detect changes in cell populations.\n\n```{r}\n\n library(CATALYST)\n library(diffcyt)\n library(imcExperiment)\n data(imcdata)\n head(rownames(imcdata))\n imcData<-imcdata\n # for plot scatter to work need to set the rowData feature in a specific way.\n channel<-sapply(strsplit(rownames(imcData),\"_\"),function(x) x[3])\n channel[34:35]<-c(\"Ir1911\",\"Ir1931\")\n marker<-sapply(strsplit(rownames(imcData),\"_\"),function(x) x[2])\n rowData(imcData)<-DataFrame(channel_name=channel,marker_name=marker)\n rownames(imcData)<-marker\n plotScatter(imcData,rownames(imcData)[17:18],assay='counts')\n\n # convert to flowSet\n ## the warning has to do with duplicated Iridium channels.\n (fsimc <- sce2fcs(imcData, split_by = \"ROIID\"))\n ## now we have a flowSet.\n pData(fsimc)\n fsApply(fsimc,nrow)\n dim(exprs(fsimc[[1]]))\n exprs(fsimc[[1]])[1:5,1:5]\n ## set up the metadata files.\n head(marker_info)\n \n exper_info<-data.frame(group_id=colData(imcData)$Treatment[match(pData(fsimc)$name,\n colData(imcData)$ROIID)],\n patient_id=colData(imcData)$Patient.Number[match(pData(fsimc)$name,\n colData(imcData)$ROIID)],\n sample_id=pData(fsimc)$name)\n \n ## create design\n design<-createDesignMatrix(\n exper_info,cols_design=c(\"group_id\",\"patient_id\"))\n \n ##set up contrast \n contrast<-createContrast(c(0,1,0))\n nrow(contrast)==ncol(design)\n data.frame(parameters=colnames(design),contrast)\n \n ## flowSet to DiffCyt\n out_DA<-diffcyt(\n d_input=fsimc,\n experiment_info=exper_info,\n marker_info=marker_info,\n design=design,\n contrast=contrast,\n analysis_type = \"DA\",\n seed_clustering = 123\n )\n topTable(out_DA,format_vals = TRUE)\n \n out_DS<-diffcyt(\n d_input=fsimc,\n experiment_info=exper_info,\n marker_info=marker_info,\n design=design,\n contrast=contrast,\n analysis_type='DS',\n seed_clustering = 123,\n plot=FALSE)\n \n topTable(out_DS,format_vals = TRUE)\n```\n ","jobInfo":{"package":"imcExperiment","version":"0.99.0","parsingStatus":"success","parserVersion":1,"parsedAt":"2021-08-19T11:30:07+0000"}}

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