[R] some help regarding combining columns from different files
Harikrishnadhar
hari.bombex at gmail.com
Tue Jan 12 22:48:36 CET 2010
Hi Jim,
I am want to merge two files into one file :
Here is my code . But the problem with this is that I am getting the 2nd
file appended to the first when i write temp3 in my code to the text file. I
am not sure what mistake I am doing .
also find the test files to run the code .
Please help me with this !!!!!!!!!!!!!!!!!!!!!!!
temp1 <- NULL
temp2 <- NULL
x.col.names <-c("genesymbol","geneDescription","orgSymbol","orgName")
y.col.names <- c("genesymbol","geneDescription","orgSymbol","orgName")
for (i in 1:length(list1.bp.files.names)){
temp1 <-
read.table(list1.bp.files.names[i],sep="\t",header=T,stringsAsFactors=F,quote="\"")
for (j in 1:length(list2.bp.files.names)){
temp2 <-
read.table(list2.bp.files.names[j],sep="\t",header=T,stringsAsFactors=F,quote="\"")
temp3 <- merge(temp1,temp2,by.x = x.col.names,by.y=y.col.names,all=T)
myfile<-gsub("( )", "", paste("1_",merge.bp.files.names[i],".txt"))
write.table(temp3,file=myfile,sep="\t",quote=FALSE,row.names=F)
}
}
Thanks
--Hari--
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genesymbol geneDescription orgSymbol orgName
E2f5 e2f transcription factor 5 RG Rattus norvegicus
Msh2 muts homolog 2 (e. coli) RG Rattus norvegicus
Kpna2 karyopherin (importin) alpha 2 RG Rattus norvegicus
Gtpbp4 gtp binding protein 4 RG Rattus norvegicus
Dtymk_predicted deoxythymidylate kinase (predicted) RG Rattus norvegicus
Ruvbl1 ruvb-like protein 1 RG Rattus norvegicus
Cetn2 centrin 2 RG Rattus norvegicus
Foxm1 forkhead box m1 RG Rattus norvegicus
Abtb1 ankyrin repeat and btb (poz) domain containing 1 RG Rattus norvegicus
Myc myelocytomatosis viral oncogene homolog (avian) RG Rattus norvegicus
Il1b interleukin 1 beta RG Rattus norvegicus
Cdc20 cell division cycle 20 homolog (s. cerevisiae) RG Rattus norvegicus
Cdc25a cell division cycle 25 homolog a (s. cerevisiae) RG Rattus norvegicus
Kifc1 kinesin family member c1 RG Rattus norvegicus
Fancd2 fanconi anemia d2 protein RG Rattus norvegicus
Rhob rhob gene RG Rattus norvegicus
Clp1 cardiac lineage protein 1 RG Rattus norvegicus
Psmd1 proteasome (prosome, macropain) 26s subunit, non-atpase, 1 RG Rattus norvegicus
Mad2l1_predicted mad2 (mitotic arrest deficient, homolog)-like 1 (yeast) (predicted) RG Rattus norvegicus
Dhcr24 24-dehydrocholesterol reductase RG Rattus norvegicus
Ahr aryl hydrocarbon receptor RG Rattus norvegicus
Rnd3 ras homolog gene family, member e RG Rattus norvegicus
Acvr1b activin a receptor, type 1b RG Rattus norvegicus
Mcm2_predicted minichromosome maintenance deficient 2 mitotin (s. cerevisiae) (predicted) RG Rattus norvegicus
Mapre3 microtubule-associated protein, rp/eb family, member 3 RG Rattus norvegicus
Mapre1 microtubule-associated protein, rp/eb family, member 1 RG Rattus norvegicus
Tardbp tar dna binding protein RG Rattus norvegicus
Cdca3 cell division cycle associated 3 RG Rattus norvegicus
Ccnb1 cyclin b1 RG Rattus norvegicus
Npm1 nucleophosmin 1 RG Rattus norvegicus
Pcaf p300/cbp-associated factor RG Rattus norvegicus
Cdc2a cell division cycle 2 homolog a (s. pombe) RG Rattus norvegicus
Dnajc2 dnaj (hsp40) homolog, subfamily c, member 2 RG Rattus norvegicus
Dab2ip disabled homolog 2 (drosophila) interacting protein RG Rattus norvegicus
Id2 inhibitor of dna binding 2, dominant negative helix-loop-helix protein RG Rattus norvegicus
Kif23_predicted kinesin family member 23 (predicted) RG Rattus norvegicus
Nek6 nima (never in mitosis gene a)-related expressed kinase 6 RG Rattus norvegicus
Pola1 polymerase (dna directed), alpha 1 RG Rattus norvegicus
Il1a interleukin 1 alpha RG Rattus norvegicus
Ccnc cyclin c RG Rattus norvegicus
Ccnb2 cyclin b2 RG Rattus norvegicus
Pbef1 pre-b-cell colony enhancing factor 1 RG Rattus norvegicus
Rad17 rad17 homolog (s. pombe) RG Rattus norvegicus
Racgap1_predicted rac gtpase-activating protein 1 (predicted) RG Rattus norvegicus
Ccna2 cyclin a2 RG Rattus norvegicus
Cdca8 cell division cycle associated 8 RG Rattus norvegicus
Sesn1_predicted sestrin 1 (predicted) RG Rattus norvegicus
Tpx2_predicted tpx2, microtubule-associated protein homolog (xenopus laevis) (predicted) RG Rattus norvegicus
Dmtf1 cyclin d binding myb-like transcription factor 1 RG Rattus norvegicus
Chek1 checkpoint kinase 1 homolog (s. pombe) RG Rattus norvegicus
Mlh1 mutl homolog 1 (e. coli) RG Rattus norvegicus
Cgref1 cell growth regulator with ef hand domain 1 RG Rattus norvegicus
Nek2 nima (never in mitosis gene a)-related expressed kinase 2 RG Rattus norvegicus
Tbrg1 transforming growth factor beta regulated gene 1 RG Rattus norvegicus
Kif2c kinesin-related protein 2 RG Rattus norvegicus
Akap8 a kinase (prka) anchor protein 8 RG Rattus norvegicus
Zw10 zw10 homolog, centromere/kinetochore protein (drosophila) RG Rattus norvegicus
Fabp1 fatty acid binding protein 1, liver RG Rattus norvegicus
Pa2g4 proliferation-associated 2g4 RG Rattus norvegicus
Myh9 myosin, heavy polypeptide 9 RG Rattus norvegicus
Mdc1 mediator of dna damage checkpoint 1 RG Rattus norvegicus
Cdk2 cyclin dependent kinase 2 RG Rattus norvegicus
Steap3 tumor suppressor phyde RG Rattus norvegicus
Vegfa vascular endothelial growth factor a RG Rattus norvegicus
Gadd45a growth arrest and dna-damage-inducible 45 alpha RG Rattus norvegicus
Anp32b acidic nuclear phosphoprotein 32 family, member b RG Rattus norvegicus
Cdk4 cyclin-dependent kinase 4 RG Rattus norvegicus
Bub1_predicted budding uninhibited by benzimidazoles 1 homolog (s. cerevisiae) (predicted) RG Rattus norvegicus
Cdkn1a cyclin-dependent kinase inhibitor 1a RG Rattus norvegicus
Uhrf1 ubiquitin-like, containing phd and ring finger domains, 1 (mapped) RG Rattus norvegicus
Tcf3_predicted transcription factor 3 (predicted) RG Rattus norvegicus
Snf1lk snf1-like kinase RG Rattus norvegicus
Stmn1 stathmin 1 RG Rattus norvegicus
Eml4_predicted echinoderm microtubule associated protein like 4 (predicted) RG Rattus norvegicus
Cenpe_predicted centromere protein e (predicted) RG Rattus norvegicus
Ppm1g protein phosphatase 1g (formerly 2c), magnesium-dependent, gamma isoform RG Rattus norvegicus
Hgf hepatocyte growth factor RG Rattus norvegicus
Mapk14 mitogen activated protein kinase 14 RG Rattus norvegicus
Nbn nibrin RG Rattus norvegicus
Ccnl1 cyclin l1 RG Rattus norvegicus
E2f1 e2f transcription factor 1 RG Rattus norvegicus
Nasp nuclear autoantigenic sperm protein RG Rattus norvegicus
Bmp2 bone morphogenetic protein 2 RG Rattus norvegicus
Bard1 brca1 associated ring domain 1 RG Rattus norvegicus
Acvr1 activin a receptor, type 1 RG Rattus norvegicus
Xpc_predicted xeroderma pigmentosum, complementation group c (predicted) RG Rattus norvegicus
Cdc26 cell division cycle 26 RG Rattus norvegicus
Ptp4a1 protein tyrosine phosphatase 4a1 RG Rattus norvegicus
Ttk_predicted ttk protein kinase (predicted) RG Rattus norvegicus
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genesymbol geneDescription orgSymbol orgName
Fdft1 farnesyl diphosphate farnesyl transferase 1 RG Rattus norvegicus
Sc4mol sterol-c4-methyl oxidase-like RG Rattus norvegicus
Fbp1 fructose-1,6- biphosphatase 1 RG Rattus norvegicus
Acat2 similar to acetyl coa transferase-like RG Rattus norvegicus
Impa1 inositol (myo)-1(or 4)-monophosphatase 1 RG Rattus norvegicus
Pmm2_predicted phosphomannomutase 2 (predicted) RG Rattus norvegicus
G6pc glucose-6-phosphatase, catalytic RG Rattus norvegicus
Pklr pyruvate kinase, liver and red blood cell RG Rattus norvegicus
Apoa2 apolipoprotein a-ii RG Rattus norvegicus
Tgfb2 transforming growth factor, beta 2 RG Rattus norvegicus
Gpi glucose phosphate isomerase RG Rattus norvegicus
Ca5a carbonic anhydrase 5 RG Rattus norvegicus
Irs2 insulin receptor substrate 2 RG Rattus norvegicus
Insig2 insulin induced gene 2 RG Rattus norvegicus
Dgat2 diacylglycerol o-acyltransferase homolog 2 (mouse) RG Rattus norvegicus
Dhcr7 7-dehydrocholesterol reductase RG Rattus norvegicus
Sphk2 sphingosine kinase 2 RG Rattus norvegicus
Cpt1a carnitine palmitoyltransferase 1, liver RG Rattus norvegicus
Tm7sf2 transmembrane 7 superfamily member 2 RG Rattus norvegicus
Sds serine dehydratase RG Rattus norvegicus
Idi1 isopentenyl-diphosphate delta isomerase RG Rattus norvegicus
Chdh choline dehydrogenase RG Rattus norvegicus
Comt catechol-o-methyltransferase RG Rattus norvegicus
Aldoa aldolase a RG Rattus norvegicus
Acaa2 acetyl-coenzyme a acyltransferase 2 (mitochondrial 3-oxoacyl-coenzyme a thiolase) RG Rattus norvegicus
Igfbp1 insulin-like growth factor binding protein 1 RG Rattus norvegicus
Dlat dihydrolipoamide s-acetyltransferase (e2 component of pyruvate dehydrogenase complex) RG Rattus norvegicus
Mdh1 malate dehydrogenase 1, nad (soluble) RG Rattus norvegicus
Pkm2 pyruvate kinase, muscle RG Rattus norvegicus
Man2b1 mannosidase 2, alpha b1 RG Rattus norvegicus
Pcyt2 phosphate cytidylyltransferase 2, ethanolamine RG Rattus norvegicus
Aldh2 aldehyde dehydrogenase 2 RG Rattus norvegicus
Ddc dopa decarboxylase RG Rattus norvegicus
Prkaa1 protein kinase, amp-activated, alpha 1 catalytic subunit RG Rattus norvegicus
Pdk2 pyruvate dehydrogenase kinase, isoenzyme 2 RG Rattus norvegicus
Pmvk phosphomevalonate kinase RG Rattus norvegicus
Mvd mevalonate (diphospho) decarboxylase RG Rattus norvegicus
Ugp2 udp-glucose pyrophosphorylase 2 RG Rattus norvegicus
Pctp phosphatidylcholine transfer protein RG Rattus norvegicus
Atf3 activating transcription factor 3 RG Rattus norvegicus
Dhtkd1 dehydrogenase e1 and transketolase domain containing 1 RG Rattus norvegicus
Gata3 gata binding protein 3 RG Rattus norvegicus
Ippk similar to chromosome 9 open reading frame 12; 1,3,4,5,6-pentakisphosphate 2-kinase RG Rattus norvegicus
Ywhah tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide RG Rattus norvegicus
Aldh5a1 aldehyde dehydrogenase family 5, subfamily a1 RG Rattus norvegicus
Hmgcs1 3-hydroxy-3-methylglutaryl-coenzyme a synthase 1 RG Rattus norvegicus
Sult1b1 sulfotransferase family 1b, member 1 RG Rattus norvegicus
Ugdh udp-glucose dehydrogenase RG Rattus norvegicus
Hmgcs2 3-hydroxy-3-methylglutaryl-coenzyme a synthase 2 RG Rattus norvegicus
Sec14l2 sec14-like 2 (s. cerevisiae) RG Rattus norvegicus
Gck glucokinase RG Rattus norvegicus
Ch25h cholesterol 25-hydroxylase RG Rattus norvegicus
Hsd17b7 hydroxysteroid (17-beta) dehydrogenase 7 RG Rattus norvegicus
Crem camp responsive element modulator RG Rattus norvegicus
Tat tyrosine aminotransferase RG Rattus norvegicus
Ldha lactate dehydrogenase a RG Rattus norvegicus
Coq7 demethyl-q 7 RG Rattus norvegicus
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genesymbol geneDescription orgSymbol orgName
E2f5 e2f transcription factor 5 RG Rattus norvegicus
Aatf apoptosis antagonizing transcription factor RG Rattus norvegicus
Numa1 nuclear mitotic apparatus protein 1 RG Rattus norvegicus
RGD1305526_predicted similar to sperm 1 pou-domain transcription factor (sprm-1) (predicted) RG Rattus norvegicus
Kpna2 karyopherin (importin) alpha 2 RG Rattus norvegicus
Anapc4 anaphase promoting complex subunit 4 RG Rattus norvegicus
Gtpbp4 gtp binding protein 4 RG Rattus norvegicus
Mki67_predicted antigen identified by monoclonal antibody ki-67 (predicted) RG Rattus norvegicus
Brca1 hypothetical gene supported by nm_012514 RG Rattus norvegicus
Cited2 cbp/p300-interacting transactivator, with glu/asp-rich carboxy-terminal domain, 2 RG Rattus norvegicus
Rbl2 retinoblastoma-like 2 RG Rattus norvegicus
Ppp2ca protein phosphatase 2a, catalytic subunit, alpha isoform RG Rattus norvegicus
Aurkb aurora kinase b RG Rattus norvegicus
RGD1307084 family with sequence similarity 33, member a RG Rattus norvegicus
Brip1_predicted brca1 interacting protein c-terminal helicase 1 (predicted) RG Rattus norvegicus
Ccng2_predicted cyclin g2 (predicted) RG Rattus norvegicus
Tgfb2 transforming growth factor, beta 2 RG Rattus norvegicus
Tubg1 tubulin, gamma 1 RG Rattus norvegicus
Gnl3 guanine nucleotide binding protein-like 3 (nucleolar) RG Rattus norvegicus
Keg1 kidney expressed gene 1 RG Rattus norvegicus
Cgrrf1 cell growth regulator with ring finger domain 1 RG Rattus norvegicus
Gtf2h1_predicted general transcription factor ii h, polypeptide 1 (predicted) RG Rattus norvegicus
Cetn3 centrin 3 RG Rattus norvegicus
Mphosph1_predicted m-phase phosphoprotein 1 (predicted) RG Rattus norvegicus
Prc1_predicted protein regulator of cytokinesis 1 (predicted) RG Rattus norvegicus
Flcn folliculin RG Rattus norvegicus
Map2k6 mitogen-activated protein kinase kinase 6 RG Rattus norvegicus
Calr calreticulin RG Rattus norvegicus
MGC112830 similar to transcription factor RG Rattus norvegicus
Fgf1 fibroblast growth factor 1 RG Rattus norvegicus
Top3a_predicted topoisomerase (dna) iii alpha (predicted) RG Rattus norvegicus
Egfr epidermal growth factor receptor RG Rattus norvegicus
Grlf1_predicted glucocorticoid receptor dna binding factor 1 (predicted) RG Rattus norvegicus
Itgb1 integrin beta 1 (fibronectin receptor beta) RG Rattus norvegicus
Dnaja2 dnaj (hsp40) homolog, subfamily a, member 2 RG Rattus norvegicus
Cep55 similar to chromosome 10 open reading frame 3 RG Rattus norvegicus
Dlg7_predicted discs, large homolog 7 (drosophila) (predicted) RG Rattus norvegicus
Pdgfc platelet-derived growth factor, c polypeptide RG Rattus norvegicus
Npm1 nucleophosmin 1 RG Rattus norvegicus
Lig3 ligase iii, dna, atp-dependent RG Rattus norvegicus
Psmd13_predicted proteasome (prosome, macropain) 26s subunit, non-atpase, 13 (predicted) RG Rattus norvegicus
Ccnf cyclin f RG Rattus norvegicus
Cenpf centromere autoantigen f RG Rattus norvegicus
Ppp2cb protein phosphatase 2a, catalytic subunit, beta isoform RG Rattus norvegicus
Rad51l3_predicted rad51-like 3 (s. cerevisiae) (predicted) RG Rattus norvegicus
Ccng1 cyclin g1 RG Rattus norvegicus
Btg3 b-cell translocation gene 3 RG Rattus norvegicus
Gmnn_predicted geminin (predicted) RG Rattus norvegicus
Gspt1 g1 to s phase transition 1 RG Rattus norvegicus
Cdc27 cell division cycle 27 homolog (s. cerevisiae) RG Rattus norvegicus
Wee1 wee 1 homolog (s. pombe) RG Rattus norvegicus
Ccnb2 cyclin b2 RG Rattus norvegicus
Nde1 nuclear distribution gene e homolog 1 (a nidulans) RG Rattus norvegicus
Ranbp1_predicted ran binding protein 1 (predicted) RG Rattus norvegicus
Ptpn11 protein tyrosine phosphatase, non-receptor type 11 RG Rattus norvegicus
Ccdc5 coiled-coil domain containing 5 RG Rattus norvegicus
Prmt5_predicted skb1 homolog (s. pombe) (predicted) RG Rattus norvegicus
RGD1309522 similar to hypothetical protein flj22624 RG Rattus norvegicus
Nek2 nima (never in mitosis gene a)-related expressed kinase 2 RG Rattus norvegicus
Junb jun-b oncogene RG Rattus norvegicus
Cdc25c_predicted cell division cycle 25 homolog c (s. cerevisiae) (predicted) RG Rattus norvegicus
Kntc1_predicted kinetochore associated 1 (predicted) RG Rattus norvegicus
Plk1 polo-like kinase 1 (drosophila) RG Rattus norvegicus
Inhba inhibin beta-a RG Rattus norvegicus
Rad1_predicted rad1 homolog (s. pombe) (predicted) RG Rattus norvegicus
Ccne1 cyclin e RG Rattus norvegicus
Kif22 kinesin family member 22 RG Rattus norvegicus
Gadd45g growth arrest and dna-damage-inducible 45 gamma RG Rattus norvegicus
Sugt1 sgt1, suppressor of g2 allele of skp1 (s. cerevisiae) RG Rattus norvegicus
Cdkn3_predicted cyclin-dependent kinase inhibitor 3 (predicted) RG Rattus norvegicus
Pbk_predicted pdz binding kinase (predicted) RG Rattus norvegicus
Pttg1 pituitary tumor-transforming 1 RG Rattus norvegicus
Kif11 kinesin-like 1 RG Rattus norvegicus
Ccnd1 cyclin d1 RG Rattus norvegicus
Casp3 caspase 3, apoptosis related cysteine protease RG Rattus norvegicus
Rpa1 replication protein a1 RG Rattus norvegicus
Bccip_predicted brca2 and cdkn1a interacting protein (predicted) RG Rattus norvegicus
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genesymbol geneDescription orgSymbol orgName
Adh7 alcohol dehydrogenase 7 (class iv), mu or sigma polypeptide RG Rattus norvegicus
Adh1 alcohol dehydrogenase 1 RG Rattus norvegicus
Adh4 alcohol dehydrogenase 4 (class ii), pi polypeptide RG Rattus norvegicus
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