inst/scripts/generate_extdata.R

In LISTO: Performing Comprehensive Overlap Assessments

# A self-contained script to generate the data in extdata
#
createExtData <- function(){
    if (requireNamespace(c('LISTO', 'qs2', 'scRNAseq','scuttle', 'Seurat',
                           'withr'), quietly=TRUE)){
        scObj <- scRNAseq::BaronPancreasData('human')
        scObj <- scuttle::logNormCounts(scObj)
        scObj <- Seurat::as.Seurat(scObj)

        donorMarkers <- LISTO::buildSeuratMarkerList(scObj, 'donor')
        labelMarkers <- LISTO::buildSeuratMarkerList(scObj, 'label')
        signatures <- list(
            acinarMarkers = c('PRSS1', 'KLK1', 'CTRC', 'PNLIP', 'AKR1C3',
                              'CTRB1','DUOXA2', 'ALDOB', 'REG3A', 'SERPINA3',
                              'PRSS3', 'REG1B','CFB',	'GDF15', 'MUC1',
                              'ANPEP', 'ANGPTL4', 'OLFM4','GSTA1', 'LGALS2',
                              'PDZK1IP1', 'RARRES2','CXCL17','UBD', 'GSTA2',
                              'LYZ', 'RBPJL', 'PTF1A', 'CELA3A','SPINK1',
                              'ZG16', 'CEL', 'CELA2A', 'CPB1', 'CELA1',
                              'PNLIPRP1', 'RNASE1', 'AMY2B', 'CPA2','CPA1',
                              'CELA3B','CTRB2', 'PLA2G1B', 'PRSS2', 'CLPS',
                              'REG1A', 'SYCN'),
            alphaMarkers = c('GCG', 'TTR', 'PCSK2', 'FXYD5', 'LDB2', 'MAFB',
                          'CHGA', 'SCGB2A1', 'GLS', 'FAP', 'DPP4', 'GPR119',
                          'PAX6', 'NEUROD1', 'LOXL4', 'PLCE1', 'GC', 'KLHL41',
                          'FEV', 'PTGER3', 'RFX6', 'SMARCA1', 'PGR', 'IRX1',
                          'UCP2', 'RGS4', 'KCNK16', 'GLP1R', 'ARX', 'POU3F4',
                          'RESP18', 'PYY', 'SLC38A5', 'TM4SF4', 'CRYBA2',
                          'SH3GL2','PCSK1', 'PRRG2', 'IRX2', 'ALDH1A1','PEMT',
                          'SMIM24','F10', 'SCGN', 'SLC30A8'),
            betaMarkers = c('INS', 'IAPP', 'GJD2', 'PDX1', 'SLC2A2', 'NPY',
                            'MAFA', 'PFKFB2','HOPX', 'PAX6', 'MAFB', 'CASR',
                            'EDARADD', 'SCGB2A1','TGFBR3','ADCYAP1', 'SH3GL2',
                            'NEUROD1', 'ISL1', 'RGS16','SMAD9', 'SIX3','BMP5',
                            'PIR', 'STXBP5', 'DLK1', 'MEG3','GCGR', 'LMX1A',
                            'JPH3', 'CD40', 'HAMP','EZH1', 'NTRK1', 'FXYD2',
                            'RIMS1', 'EFNA5', 'NPTX2', 'PAX4', 'PCSK2',
                            'G6PC2', 'SLC30A8', 'PCSK1', 'SCGN', 'IGF2',
                            'SYT13', 'FFAR2', 'SIX2'),
            deltaMarkers = c('SST', 'GABRB3', 'FRZB', 'MS4A8', 'BAIAP3',
                             'CASR', 'BCHE', 'UNC5B','EDN3', 'GHSR', 'PCSK1',
                             'GABRG2', 'POU3F1', 'BHLHE41', 'EHF', 'LCORL',
                             'ETV1', 'PDX1', 'LEPR', 'UCP2', 'NPTX2', 'FXYD2',
                             'IAPP', 'KCNK16', 'SCGN', 'ISL1', 'HHEX',
                             'RESP18', 'PAX4', 'RBP4', 'PCSK9', 'FFAR4'),
            ductalMarkers =  c('CFTR', 'SERPINA5', 'SLPI', 'TFF1', 'CFB',
                               'LGALS4', 'CTSH',	'PERP', 'PDLIM3', 'WFDC2',
                               'SLC3A1', 'AQP1', 'ALDH1A3', 'VTCN1', 'KRT19',
                               'TFF2', 'KRT7', 'CLDN4', 'LAMB3', 'TACSTD2',
                               'CCL2', 'DCDC2','CXCL2', 'CLDN10', 'HNF1B',
                               'KRT20', 'MUC1', 'ONECUT1', 'AMBP', 'HHEX',
                               'ANXA4', 'SPP1', 'PDX1', 'SERPINA3', 'GDF15',
                               'AKR1C3', 'MMP7', 'DEFB1', 'SERPING1',
                               'TSPAN8', 'CLDN1', 'S100A10', 'PIGR'),
            gammaMarkers = c('PPY', 'ABCC9', 'FGB', 'ZNF503', 'MEIS1', 'LMO3',
                             'EGR3', 'CHN2', 'PTGFR', 'ENTPD2', 'AQP3',
                             'THSD7A', 'CARTPT', 'ISL1', 'PAX6', 'NEUROD1',
                             'APOBEC2', 'SEMA3E', 'SLITRK6','SERTM1', 'PXK',
                             'PPY2P', 'ETV1', 'ARX', 'CMTM8', 'SCGB2A1',
                             'FXYD2', 'SCGN'))

        qs2::qs_save(donorMarkers, 'inst/extdata/donorMarkers.qs2')
        qs2::qs_save(labelMarkers, 'inst/extdata/labelMarkers.qs2')
        qs2::qs_save(signatures, 'inst/extdata/signatures.qs2')
        qs2::qs_save(rownames(scObj), 'inst/extdata/universe1.qs2')
        qs2::qs_save(Reduce(union, signatures), 'inst/extdata/universe2.qs2')

        seuratObj <- withr::with_seed(1, scuttle::mockSCE(ngenes=500))
        seuratObj <- Seurat::as.Seurat(seuratObj, data=NULL)
        seuratObj <- Seurat::NormalizeData(seuratObj)
        qs2::qs_save(seuratObj, 'inst/extdata/seuratObj.qs2')
    }
}

createExtData()