## ---- eval = false ----------------------------------------------------＃库（Biocinstaller）＃bioclite（“链接 - ny / rtcgatoolboar”）## ----消息=假-----------------------------------------------------------------------------------图书馆（RTCGATOOLBOX）（rundates < - getfirehoserunningdates（））## ----------------------------------------------------------------（分析< - getFirehoseanalyzedates（））## ---- eval = false ----------------------------------------------------------------------＃ov < - getfirehosateata（“ov”，rundate = rundates [1]，gistic2_date = snalysdates [1]，rnaseq_gene = true，＃mirnaseq_gene = true，rnaseq2_gene_norm = true，cna_snp = true，cnv_snp = true，cna_seq = true，＃cna_cgh = true，甲基化= true，突变= true，mrna_array = true，mirna_array = true，#rppa = true，todir = null）＃＃gbm < - getfirehosateata（“gbm”，rundate = rundates [1]，gistic2_date =分析[1]，rnaseq_gene = true，＃mirnaseq_gene = true，rnaseq2_gene_norm = true，cna_snp = true，cnv_snp = true，cna_seq = true，＃cna_cgh = true，甲基化= true，mutation = true，mrna_array = true，#rppa = true，todir = null）## coad < - getFirehosateata（“coad”，rundate = rundates [1]，gistic2_date = snalysdates [1]，rnaseq_gene = true，#mirnaseq_gene = true，rnaseq2_gene_norm = true，cnv_snp = true，cnv_snp = true，cna_seq = true，#cna_seq = true，＃cna_cgh = true，emperylation = true，mrna_array = true，mirna_array = true，#rppa = true，todir = null）## LAML < - GetFireHosatia（“LAML”，Rundate = Rundates [1]，Gistic2_Date = Sialsdates [1]，rnaseq_gene = true，#mirnaseq_gene = true，rnaseq2_gene_norm = true，cna_snp = true，cnv_snp = true，cna_seq = true，＃cna_cgh = true，earmation = true，mratation = true，mrna_array = true，mirna_array = true，#rppa = true，todir = null）#blca < - getfirehosateata（“blca”，rundate = rundates [1]，gistic2_date=分析[1]，rnaseq_gene = true，＃mirnaseq_gene = true，rnaseq2_gene_norm = true，cna_snp = true，cnv_snp = true，cnv_snp = true，cna_seq = true，＃cna_cgh = true，甲基化= true，mraton = true，mrna_array = true，mirna_array = TRUE, # RPPA = TRUE, todir = NULL) ## ------------------------------------------------------------------------ library(bioc2015multiomicsworkshop) data(laml) laml ## ------------------------------------------------------------------------ choices <- tolower(gsub("_", "", c("RNAseq_Gene", "miRNASeq_Gene", "RNAseq2_Gene_Norm", "CNA_SNP", "CNV_SNP", "CNA_Seq", "CNA_CGH", "Methylation", "Mutation", "mRNA_Array", "miRNA_Array", "RPPA"))) ## ------------------------------------------------------------------------ cna <- extract(laml, "cnasnp", clinical=TRUE) cna ## ------------------------------------------------------------------------ rnaseq <- extract(laml, "rnaseqgene", clinical=TRUE) rnaseq ## ------------------------------------------------------------------------ summary(names(cna) %in% sampleNames(rnaseq)) ## ------------------------------------------------------------------------ elementMetadata(cna)[1:2, 1:4] pData(rnaseq)[1:2, 1:4]