R数据整理到差异分析

PLATFORM与注释包platformMap——果子学生信

2019-08-16  本文已影响0人  BioJournal_Link

于目标文件夹中创建platformMap.txt文本文档
复制下面文本于platformMap.txt文本文档中,保存为UTF-8编码格式

plateformMap <- data.table::fread("platformMap.txt")
platformMap <- platformMap[,-1]
"title" "gpl" "bioc_package" "manufacturer" "organism" "data_row_count" "R_package"
"1" "Illumina Sentrix Array Matrix (SAM) - GoldenGate Methylation Cancer Panel I" "GPL15380" "GGHumanMethCancerPanelv1" "Illumina" "Homo sapiens" 1536 "GGHumanMethCancerPanelv1.db"
"2" "Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2)" "GPL8490" "IlluminaHumanMethylation27k" "Illumina, Inc." "Homo sapiens" 27578 "IlluminaHumanMethylation27k.db"
"3" "Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)" "GPL13534" "IlluminaHumanMethylation450k" "Illumina, Inc." "Homo sapiens" 485577 "IlluminaHumanMethylation450k.db"
"4" "GE Healthcare/Amersham Biosciences CodeLink™   ADME Rat 16-Assay Bioarray" "GPL2898" "adme16cod" "GE Healthcare" "Rattus norvegicus" 1280 "adme16cod.db"
"5" "[AG] Affymetrix Arabidopsis Genome Array" "GPL71" "ag" "Affymetrix" "Arabidopsis thaliana" 8297 "ag.db"
"6" "[ATH1-121501] Affymetrix Arabidopsis ATH1 Genome Array" "GPL198" "ath1121501" "Affymetrix" "Arabidopsis thaliana" 22810 "ath1121501.db"
"7" "[Bovine] Affymetrix Bovine Genome Array" "GPL2112" "bovine" "Affymetrix" "Bos taurus" 24128 "bovine.db"
"8" "[Canine] Affymetrix Canine Genome 1.0 Array" "GPL3979" "canine" "Affymetrix" "Canis lupus familiaris" 23913 "canine.db"
"9" "[Canine_2] Affymetrix Canine Genome 2.0 Array" "GPL3738" "canine2" "Affymetrix" "Canis lupus familiaris" 43035 "canine2.db"
"10" "[Celegans] Affymetrix C. elegans Genome Array" "GPL200" "celegans" "Affymetrix" "Caenorhabditis elegans" 22625 "celegans.db"
"11" "[Chicken] Affymetrix Chicken Genome Array" "GPL3213" "chicken" "Affymetrix" "Gallus gallus" 38535 "chicken.db"
"12" "[DrosGenome1] Affymetrix Drosophila Genome Array" "GPL72" "drosgenome1" "Affymetrix" "Drosophila melanogaster" 14010 "drosgenome1.db"
"13" "[Drosophila_2] Affymetrix Drosophila Genome 2.0 Array" "GPL1322" "drosophila2" "Affymetrix" "Drosophila melanogaster" 18952 "drosophila2.db"
"14" "[Ecoli_ASv2] Affymetrix E. coli Antisense Genome Array" "GPL199" "ecoli2" "Affymetrix" "Escherichia coli K-12" 7312 "ecoli2.db"
"15" "CodeLink UniSet Human I Bioarray" "GPL4191" "h10kcod" "GE Healthcare" "Homo sapiens" 10458 "h10kcod.db"
"16" "GE Healthcare/Amersham Biosciences CodeLink™   UniSet Human 20K I Bioarray" "GPL2891" "h20kcod" "GE Healthcare" "Homo sapiens" 23572 "h20kcod.db"
"17" "[HC_G110] Affymetrix Human Cancer Array" "GPL74" "hcg110" "Affymetrix" "Homo sapiens" 2059 "hcg110.db"
"18" "[HG-Focus] Affymetrix Human HG-Focus Target Array" "GPL201" "hgfocus" "Affymetrix" "Homo sapiens" 8793 "hgfocus.db"
"19" "[HG-U133A] Affymetrix Human Genome U133A Array" "GPL96" "hgu133a" "Affymetrix" "Homo sapiens" 22283 "hgu133a.db"
"20" "[HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array" "GPL571" "hgu133a2" "Affymetrix" "Homo sapiens" 22277 "hgu133a2.db"
"21" "[HG-U133B] Affymetrix Human Genome U133B Array" "GPL97" "hgu133b" "Affymetrix" "Homo sapiens" 22645 "hgu133b.db"
"22" "[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array" "GPL570" "hgu133plus2" "Affymetrix" "Homo sapiens" 54675 "hgu133plus2.db"
"23" "[HG-U219] Affymetrix Human Genome U219 Array" "GPL13667" "hgu219" "Affymetrix" "Homo sapiens" 49386 "hgu219.db"
"24" "[HG_U95A] Affymetrix Human Genome U95A Array" "GPL91" "hgu95av2" "Affymetrix" "Homo sapiens" 12626 "hgu95av2.db"
"25" "[HG_U95Av2] Affymetrix Human Genome U95 Version 2 Array" "GPL8300" "hgu95av2" "Affymetrix" "Homo sapiens" 12625 "hgu95av2.db"
"26" "[HG_U95B] Affymetrix Human Genome U95B Array" "GPL92" "hgu95b" "Affymetrix" "Homo sapiens" 12620 "hgu95b.db"
"27" "[HG_U95C] Affymetrix Human Genome U95C Array" "GPL93" "hgu95c" "Affymetrix" "Homo sapiens" 12646 "hgu95c.db"
"28" "[HG_U95D] Affymetrix Human Genome U95D Array" "GPL94" "hgu95d" "Affymetrix" "Homo sapiens" 12644 "hgu95d.db"
"29" "[HG_U95E] Affymetrix Human Genome U95E Array" "GPL95" "hgu95e" "Affymetrix" "Homo sapiens" 12639 "hgu95e.db"
"30" "Agilent Human 1 cDNA Microarray (G4100A) [layout C]" "GPL5689" "hgug4100a" "Agilent Technologies" "Homo sapiens" 16281 "hgug4100a.db"
"31" "Agilent-012097 Human 1A Microarray (V2) G4110B (Feature Number version)" "GPL887" "hgug4110b" "Agilent Technologies" "Homo sapiens" 22575 "hgug4110b.db"
"32" "Agilent-011871 Human 1B Microarray G4111A (Feature Number version)" "GPL886" "hgug4111a" "Agilent Technologies" "Homo sapiens" 22575 "hgug4111a.db"
"33" "Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version)" "GPL1708" "hgug4112a" "Agilent Technologies" "Homo sapiens" 44290 "hgug4112a.db"
"34" "[HT_HG-U133A] Affymetrix Human Genome U133A Array (custom CDF: HTHGU133A_Hs_ENTREZG.cdf version 17.0.0)" "GPL17897" "hthgu133a" "Affymetrix" "Homo sapiens" 12092 "hthgu133a.db"
"35" "[HT_HG-U133B] Affymetrix HT Human Genome U133B Array [custom CDF: ENTREZ brainarray v. 14]" "GPL15396" "hthgu133b" "Affymetrix" "Homo sapiens" 7906 "hthgu133b.db"
"36" "[Hu35KsubA] Affymetrix Human 35K SubA Array" "GPL98" "hu35ksuba" "Affymetrix" "Homo sapiens" 8934 "hu35ksuba.db"
"37" "[Hu35KsubB] Affymetrix Human 35K SubB Array" "GPL99" "hu35ksubb" "Affymetrix" "Homo sapiens" 8924 "hu35ksubb.db"
"38" "[Hu35KsubC] Affymetrix Human 35K SubC Array" "GPL100" "hu35ksubc" "Affymetrix" "Homo sapiens" 8928 "hu35ksubc.db"
"39" "[Hu35KsubD] Affymetrix Human 35K SubD Array" "GPL101" "hu35ksubd" "Affymetrix" "Homo sapiens" 8928 "hu35ksubd.db"
"40" "[Hu6800] Affymetrix Human Full Length HuGeneFL Array" "GPL80" "hu6800" "Affymetrix" "Homo sapiens" 7129 "hu6800.db"
"41" "[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version]" "GPL6244" "hugene10sttranscriptcluster" "Affymetrix" "Homo sapiens" 33297 "hugene10sttranscriptcluster.db"
"42" "[HuGene-1_1-st] Affymetrix Human Gene 1.1 ST Array [transcript (gene) version]" "GPL11532" "hugene11sttranscriptcluster" "Affymetrix" "Homo sapiens" 33297 "hugene11sttranscriptcluster.db"
"43" "Illumina human-6 v1.0 expression beadchip" "GPL6097" "illuminaHumanv1" "Illumina Inc." "Homo sapiens" 47296 "illuminaHumanv1.db"
"44" "Illumina human-6 v2.0 expression beadchip" "GPL6102" "illuminaHumanv2" "Illumina Inc." "Homo sapiens" 48702 "illuminaHumanv2.db"
"45" "Illumina HumanHT-12 V3.0 expression beadchip" "GPL6947" "illuminaHumanv3" "Illumina Inc." "Homo sapiens" 49576 "illuminaHumanv3.db"
"46" "Illumina HumanHT-12 V4.0 expression beadchip" "GPL10558" "illuminaHumanv4" "Illumina Inc." "Homo sapiens" 47323 "illuminaHumanv4.db"
"47" "[MG_U74A] Affymetrix Murine Genome U74A Array" "GPL32" "mgu74a" "Affymetrix" "Mus musculus" 12654 "mgu74a.db"
"48" "[MG_U74Av2] Affymetrix Murine Genome U74A Version 2 Array" "GPL81" "mgu74av2" "Affymetrix" "Mus musculus" 12488 "mgu74av2.db"
"49" "[MG_U74B] Affymetrix Murine Genome U74B Array" "GPL33" "mgu74b" "Affymetrix" "Mus musculus" 12636 "mgu74b.db"
"50" "[MG_U74Bv2] Affymetrix Murine Genome U74B Version 2 Array" "GPL82" "mgu74bv2" "Affymetrix" "Mus musculus" 12477 "mgu74bv2.db"
"51" "[MG_U74C] Affymetrix Murine Genome U74C Array" "GPL34" "mgu74c" "Affymetrix" "Mus musculus" 12728 "mgu74c.db"
"52" "[MG_U74Cv2] Affymetrix Murine Genome U74 Version 2 Array" "GPL83" "mgu74cv2" "Affymetrix" "Mus musculus" 11934 "mgu74cv2.db"
"53" "[Maize] Affymetrix Maize Genome Array" "GPL4032" "moe430a" "Affymetrix" "Zea mays" 17734 "moe430a.db"
"54" "[MOE430A] Affymetrix Mouse Expression 430A Array" "GPL339" "moe430b" "Affymetrix" "Mus musculus" 22690 "moe430b.db"
"55" "[MOE430B] Affymetrix Mouse Expression 430B Array" "GPL340" "mouse4302" "Affymetrix" "Mus musculus" 22575 "mouse4302.db"
"56" "[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array" "GPL1261" "mouse430a2" "Affymetrix" "Mus musculus" 45101 "mouse430a2.db"
"57" "[Mu11KsubA] Affymetrix Murine 11K SubA Array" "GPL75" "mu11ksuba" "Affymetrix" "Mus musculus" 6584 "mu11ksuba.db"
"58" "[Mu11KsubB] Affymetrix Murine 11K SubB Array" "GPL76" "mu11ksubb" "Affymetrix" "Mus musculus" 6595 "mu11ksubb.db"
"59" "[Mu19KsubA] Affymetrix Murine 19K SubA Array" "GPL77" "mu19ksuba" "Affymetrix" "Mus musculus" 7045 "mu19ksuba.db"
"60" "[Mu19KsubB] Affymetrix Murine 19K SubB Array" "GPL78" "mu19ksubb" "Affymetrix" "Mus musculus" 7054 "mu19ksubb.db"
"61" "[Mu19KsubC] Affymetrix Murine 19K SubC Array" "GPL79" "mu19ksubc" "Affymetrix" "Mus musculus" 7047 "mu19ksubc.db"
"62" "[RAE230A] Affymetrix Rat Expression 230A Array" "GPL341" "rae230a" "Affymetrix" "Rattus norvegicus" 15923 "rae230a.db"
"63" "[RAE230B] Affymetrix Rat Expression 230B Array" "GPL342" "rae230b" "Affymetrix" "Rattus norvegicus" 15333 "rae230b.db"
"64" "[Rat230_2] Affymetrix Rat Genome 230 2.0 Array" "GPL1355" "rat2302" "Affymetrix" "Rattus norvegicus" 31099 "rat2302.db"
"65" "[RG_U34A] Affymetrix Rat Genome U34 Array" "GPL85" "rgu34a" "Affymetrix" "Rattus norvegicus" 8799 "rgu34a.db"
"66" "[RG_U34B] Affymetrix Rat Genome U34 Array" "GPL86" "rgu34b" "Affymetrix" "Rattus norvegicus" 8791 "rgu34b.db"
"67" "[RG_U34C] Affymetrix Rat Genome U34 Array" "GPL87" "rgu34c" "Affymetrix" "Rattus norvegicus" 8789 "rgu34c.db"
"68" "[RN_U34] Affymetrix Rat Neurobiology U34 Array" "GPL88" "rnu34" "Affymetrix" "Rattus norvegicus" 1322 "rnu34.db"
"69" "[RT_U34] Affymetrix Rat Toxicology U34 Array" "GPL89" "rtu34" "Affymetrix" "Rattus norvegicus" 1031 "rtu34.db"
"70" "[U133_X3P] Affymetrix Human X3P Array" "GPL1352" "u133x3p" "Affymetrix" "Homo sapiens" 61359 "u133x3p.db"
"71" "[Xenopus_laevis] Affymetrix Xenopus laevis Genome Array" "GPL1318" "xenopuslaevis" "Affymetrix" "Xenopus laevis" 15611 "xenopuslaevis.db"
"72" "[Yeast_2] Affymetrix Yeast Genome 2.0 Array" "GPL2529" "yeast2" "Affymetrix" "Schizosaccharomyces pombe;  Saccharomyces cerevisiae" 10928 "yeast2.db"
"73" "[YG_S98] Affymetrix Yeast Genome S98 Array" "GPL90" "ygs98" "Affymetrix" "Saccharomyces cerevisiae" 9335 "ygs98.db"
"74" "[Zebrafish] Affymetrix Zebrafish Genome Array" "GPL1319" "zebrafish" "Affymetrix" "Danio rerio" 15617 "zebrafish.db"

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