目前，我有一些代码可以读取forloop中的文本文件和xlsx文件（openxlsx软件包）。我想做的是将各列加在一起并将文件输出为xlsx，覆盖原始的xlsx文件。我想在forloop中执行此操作，以使每个文件都被覆盖。
我不想将所有这些数据帧一起添加到1个巨型数据帧中，这是大多数人问这个问题时最常见的查询，我只想将txtfile添加到xlsfile并编写xlsx，覆盖旧的xlsx文件，并根据需要重复。
xls <- dir(pattern = "*xlsx")
txt <- dir(pattern = "*txt")
library("dplyr")
for (xlsfile in xls) {
D1 <- read.xlsx(xlsfile, colNames = F, rowNames = F)
for (txtfile in txt) {
D2 <- read.csv(txtfile, header=F, skip=3, colClasses=c("NULL", rep(NA,3),
rep("NULL",7), rep(NA,3), rep("NULL",6)
# this is to keep columns for D2 in line with the columns in D1
D3 <- bind_rows(D2, D1)
write.xlsx(D3, xlsfile)
}
}
我尝试使用rbind_all创建D3，但是R说rbind_all已过时？第一个问题是，当使用xlsx包读取D1时，我得到了带有X1-X6的标头，这很好，因为这是我以D2的形式在缩短的txtfile中有多少列。但是，D2的标头是V2，V3，V4，V12，V13，V14。使用bind_rows时，它以V2-4和V12-14的形式创建6个新的列标题，而不是将它们添加到X1-X6列中，因此新信息位于xlsx数据帧结束处的正下方6列。
有人告诉我，这两个文件的字符是不同的因素，我不确定这是为什么或如何发生的，而且我不相信从“ V”到“ X”的简单gsub会起作用，因为我有D2中的V后面有不同的数字。
但是，forloop仍然与bind_rows一起运行，并且由于某种原因，当我打开用旧文件编写的xlsx文件时，它们都包含与最后一个xlsfile + txtfile相同的信息和元素，这意味着所有新的xlsx文件与我的文件完全相同，并包含我的最后文件信息，但仍带有多余的列。我相信这是我的代码的一个单独问题，但是我不确定如何创建它，以便它不会一遍又一遍地重新创建最后一个文件。我认为这是由我的代码引起的，在某些时候，forloop完成了D3的创建，但尚未编写xlsx文件，然后它遍历了write.xlsx函数。
这是R中的xlsx（D1）文件。
structure(list(X1 = c("#version 2.4", "## Oncotator v1.5.3.0 | Flat File
Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | CCLE_By_GP
09292010 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | dbSNP build
142 | 1000Genome phase3 20130502 | ClinVar 12.03.20 | COSMIC v62_291112 |
ORegAnno UCSC Track | ESP 6500SI-V2 | UniProt 2014_12 | HumanDNARepairGenes
20110905 | TUMORScape 20100104 | CCLE_By_Gene 09292010 | MutSig Published
Results 20110905 | COSMIC_Tissue 291112 | CGC full_2012-03-15 |
COSMIC_FusionGenes v62_291112 | HGNC Sept172014 | ACHILLES_Lineage_Results
110303 | TCGAScape 110405 | Ensembl ICGC MUCOPA | Familial_Cancer_Genes
20110905 | gencode_xref_refseq metadata_v19 ",
"Hugo_Symbol", "MTOR", "EPHA2", "ARID1A"), X2 = c("P3F5", NA,
"Chromosome", "1", "1", "1"), X3 = c(NA, NA, "Start_position",
"11307916", "16464389", "27107273"), X4 = c(NA, NA, "End_position",
"11307916", "16464389", "27107273"), X5 = c(NA, NA,
"Variant_Classification",
"Missense_Mutation", "Missense_Mutation", "3'UTR"), X6 = c(NA,
NA, "Variant_Type", "SNP", "SNP", "SNP"), X7 = c(NA, NA, "Reference_Allele",
"C", "C", "G"), X8 = c(NA, NA, "Tumor_Seq_Allele2", "T", "T",
"C"), X9 = c(NA, NA, "dbSNP_RS", NA, NA, "rs199555039"), X10 = c(NA,
NA, "dbSNP_Val_Status", NA, NA, "byFrequency"), X11 = c(NA, NA,
"Genome_Change", "g.chr1:11307916C>T", "g.chr1:16464389C>T",
"g.chr1:27107273G>C"), X12 = c(NA, NA, "Protein_Change", "p.S359N",
"p.S424N", NA), X13 = c(NA, NA, "COSMIC_overlapping_mutations",
NA, NA, NA)), .Names = c("X1", "X2", "X3", "X4", "X5", "X6",
"X7", "X8", "X9", "X10", "X11", "X12", "X13"), row.names = c(NA,
6L), class = "data.frame")
和缩短为D2的txtfile是
structure(list(V1 = structure(c(2L, 1L, 31L, 41L), .Label = c("##
Oncotator v1.5.3.0 | Flat File Reference hg19 | GENCODE v19 EFFECT |
UniProt_AAxform 2014_12 | CCLE_By_GP 09292010 | UniProt_AA 2014_12 | dbNSFP
v2.4 | ESP 6500SI-V2 | dbSNP build 142 | 1000Genome phase3 20130502 |
ClinVar 12.03.20 | COSMIC v62_291112 | ORegAnno UCSC Track | ESP 6500SI-V2 |
UniProt 2014_12 | HumanDNARepairGenes 20110905 | TUMORScape 20100104 |
CCLE_By_Gene 09292010 | MutSig Published Results 20110905 | COSMIC_Tissue
291112 | CGC full_2012-03-15 | COSMIC_FusionGenes v62_291112 | HGNC
Sept172014 | ACHILLES_Lineage_Results 110303 | TCGAScape 110405 | Ensembl
ICGC MUCOPA | Familial_Cancer_Genes 20110905 | gencode_xref_refseq
metadata_v19 ",
"#version 2.4", "ALK", "APC", "ARID1A", "ATM", "BAP1", "BCOR",
"C11orf30", "CDH1", "CDKN2B-AS1", "CHD1", "CNOT3", "CSF3R", "CTNNB1",
"DOK6", "EP300", "EPCAM", "EPHA2", "EPHA7", "EPOR", "ERBB2",
"ERCC2", "ETV6", "FANCA", "FGF6", "FOXO1", "GPR124", "HDAC4",
"HNF1A", "Hugo_Symbol", "IKBKE", "KDM5C", "KDR", "KLF4", "KMT2B",
"KMT2D", "LRP1B", "MAP2K4", "MET", "MTOR", "MYB", "NCOA3", "NF2",
"NOTCH2", "NSD1", "NTRK2", "NTRK3", "NUTM1", "PARK2", "PAX8",
"PBRM1", "PDGFRA", "PDGFRB", "PHF8", "PMS1", "PMS2", "POLE",
"POT1", "PRKCA", "RAD51C", "RAF1", "RB1", "ROBO1", "RUNX1", "SLIT2",
"SMC1A", "SYK", "SYNE1", "TCF7L2", "TP53", "Unknown", "USP7",
"WHSC1", "ZMYM3"), class = "factor"), V5 = structure(c(1L, 1L,
23L, 2L), .Label = c("", "1", "10", "11", "12", "13", "15", "16",
"17", "18", "19", "2", "20", "21", "22", "3", "4", "5", "6",
"7", "8", "9", "Chromosome", "X"), class = "factor"), V6 = structure(c(1L,
1L, 99L, 6L), .Label = c("", "108121722", "110249856", "112174416",
"112175711", "11307916", "113991570", "114849135", "11488524",
"116418878", "11958126", "12038916", "120510314", "121426926",
"123011945", "124481159", "12626167", "12641934", "12642536",
"12650654", "133240692", "135537281", "141806602", "144003367",
"149495558", "152646204", "161771035", "16464389", "172516645",
"176636762", "190728482", "1918738", "20597970", "206666682",
"22103913", "240003706", "27107273", "29432715", "29445154",
"29541192", "30038169", "31526940", "34508048", "34646113", "34649335",
"36176975", "36186234", "36193590", "36210950", "36937111", "37689156",
"37884417", "39921415", "41162692", "41193074", "41217841", "41223629",
"41266049", "41564531", "4554585", "45867603", "46264182", "47613623",
"48955624", "49439908", "51012853", "52442493", "52501682", "52692305",
"53225043", "53441750", "54008382", "54647625", "55133866", "55970836",
"56774005", "6029518", "64685656", "64691239", "64695929", "64711567",
"64723880", "67511099", "68863633", "70465919", "7588995", "76164351",
"79067483", "87476563", "88663732", "89849429", "89851191", "9017149",
"92561683", "93657891", "93969298", "98194682", "98209419", "Start_position"
), class = "factor"), V7 = structure(c(1L, 1L, 99L, 6L), .Label = c("",
"108121722", "110249856", "112174416", "112175711", "11307916",
"113991570", "114849135", "11488524", "116418878", "11958126",
"12038916", "120510314", "121426926", "123011945", "124481159",
"12626167", "12641934", "12642536", "12650654", "133240692",
"135537281", "141806602", "144003367", "149495558", "152646204",
"161771035", "16464389", "172516645", "176636762", "190728482",
"1918738", "20597970", "206666682", "22103913", "240003706",
"27107273", "29432715", "29445154", "29541192", "30038169", "31526940",
"34508048", "34646113", "34649335", "36176975", "36186234", "36193590",
"36210950", "36937111", "37689156", "37884417", "39921415", "41162692",
"41193074", "41217841", "41223629", "41266049", "41564531", "4554585",
"45867603", "46264182", "47613623", "48955624", "49439908", "51012853",
"52442493", "52501682", "52692305", "53225043", "53441750", "54008382",
"54647625", "55133866", "55970836", "56774005", "6029518", "64685656",
"64691239", "64695929", "64711567", "64723880", "67511099", "68863633",
"70465919", "7588995", "76164351", "79067483", "87476563", "88663732",
"89849429", "89851191", "9017149", "92561683", "93657891", "93969298",
"98194682", "98209419", "End_position"), class = "factor"), V9 =
structure(c(1L,
1L, 9L, 5L), .Label = c("", "3'UTR", "IGR", "Intron", "Missense_Mutation",
"Nonsense_Mutation", "RNA", "Silent", "Variant_Classification"
), class = "factor"), V10 = structure(c(1L, 1L, 3L, 2L), .Label = c("",
"SNP", "Variant_Type"), class = "factor"), V11 = structure(c(1L,
1L, 5L, 3L), .Label = c("", "A", "C", "G", "Reference_Allele",
"T"), class = "factor"), V13 = structure(c(1L, 1L, 6L, 5L), .Label = c("",
"A", "C", "G", "T", "Tumor_Seq_Allele2"), class = "factor"),
V14 = structure(c(1L, 1L, 2L, 1L), .Label = c("", "dbSNP_RS",
"rs116809738", "rs139387758", "rs141802026", "rs150631563",
"rs199555039", "rs372456536", "rs550515708", "rs567211112",
"rs571512044", "rs587782826", "rs79547774"), class = "factor"),
V15 = structure(c(1L, 1L, 3L, 1L), .Label = c("", "byFrequency",
"dbSNP_Val_Status"), class = "factor"), V35 = structure(c(1L,
1L, 99L, 2L), .Label = c("", "g.chr1:11307916C>T", "g.chr1:120510314G>A",
"g.chr1:16464389C>T", "g.chr1:206666682C>A", "g.chr1:27107273G>C",
"g.chr1:36937111G>T", "g.chr10:114849135G>A", "g.chr10:123011945G>A",
"g.chr11:108121722C>T", "g.chr11:76164351T>A", "g.chr12:12038916A>G",
"g.chr12:121426926A>C", "g.chr12:133240692C>T", "g.chr12:4554585G>A",
"g.chr12:49439908G>A", "g.chr13:41162692A>G", "g.chr13:41193074G>A",
"g.chr13:41217841T>C", "g.chr13:41223629G>T", "g.chr13:48955624C>T",
"g.chr15:34646113G>A", "g.chr15:34649335T>C", "g.chr15:88663732G>A",
"g.chr16:31526940C>T", "g.chr16:68863633T>A", "g.chr16:89849429G>A",
"g.chr16:89851191C>T", "g.chr16:9017149C>T", "g.chr17:11958126G>A",
"g.chr17:37884417C>T", "g.chr17:56774005C>T", "g.chr17:64685656C>T",
"g.chr17:64691239G>A", "g.chr17:64695929A>T", "g.chr17:64711567C>T",
"g.chr17:64723880G>A", "g.chr17:7588995C>T", "g.chr18:67511099A>G",
"g.chr19:11488524C>T", "g.chr19:34508048G>A", "g.chr19:36210950A>G",
"g.chr19:45867603A>G", "g.chr19:54647625C>T", "g.chr2:113991570C>T",
"g.chr2:141806602C>T", "g.chr2:190728482G>A", "g.chr2:240003706G>A",
"g.chr2:29432715G>A", "g.chr2:29445154C>T", "g.chr2:29541192G>T",
"g.chr2:47613623A>C", "g.chr20:46264182A>C", "g.chr20:51012853G>A",
"g.chr20:52501682G>A", "g.chr21:36176975G>A", "g.chr21:36186234T>G",
"g.chr21:36193590A>G", "g.chr22:30038169T>C", "g.chr22:41564531C>T",
"g.chr3:12626167G>A", "g.chr3:12641934C>T", "g.chr3:12642536G>T",
"g.chr3:12650654C>T", "g.chr3:41266049C>G", "g.chr3:52442493G>A",
"g.chr3:52692305G>A", "g.chr3:79067483T>C", "g.chr4:172516645G>A",
"g.chr4:1918738G>A", "g.chr4:20597970G>A", "g.chr4:55133866T>C",
"g.chr4:55970836C>T", "g.chr5:112174416G>T", "g.chr5:112175711G>A",
"g.chr5:149495558A>G", "g.chr5:176636762T>C", "g.chr5:98194682A>G",
"g.chr5:98209419G>A", "g.chr6:135537281C>T", "g.chr6:152646204G>A",
"g.chr6:161771035C>T", "g.chr6:93969298C>G", "g.chr7:116418878T>A",
"g.chr7:124481159G>T", "g.chr7:6029518C>T", "g.chr7:92561683G>A",
"g.chr8:144003367A>G", "g.chr8:37689156T>A", "g.chr9:110249856C>T",
"g.chr9:22103913G>A", "g.chr9:87476563G>A", "g.chr9:93657891G>A",
"g.chrX:39921415G>A", "g.chrX:53225043G>A", "g.chrX:53441750T>C",
"g.chrX:54008382T>C", "g.chrX:70465919G>A", "Genome_Change"
), class = "factor"), V42 = structure(c(1L, 1L, 40L, 34L), .Label = c("",
"p.A1150V", "p.A1474T", "p.A301T", "p.A353T", "p.A403D",
"p.A510A", "p.A624T", "p.C654Y", "p.D1014D", "p.D454D", "p.G581D",
"p.H84H", "p.I1148N", "p.I185I", "p.K123R", "p.K234R", "p.K403K",
"p.L360P", "p.L413I", "p.L518L", "p.L791H", "p.L868L", "p.M102I",
"p.P16A", "p.P542Q", "p.P672P", "p.P868S", "p.Q1545*", "p.Q410P",
"p.R1469W", "p.S1042I", "p.S1318L", "p.S359N", "p.S424N",
"p.S51L", "p.T1258I", "p.T273T", "p.V1521A", "Protein_Change"
), class = "factor"), V57 = structure(c(1L, 1L, 2L, 1L), .Label = c("",
"COSMIC_overlapping_mutations", "p.?(1)", "p.?(2)", "p.0?(10)|p.?(1)",
"p.0?(15)|p.?(4)", "p.0?(2)|p.?(1)", "p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.?(4)|p.T3_A126del(2)|p.A5fs*7(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.D6_S29del(1)|p.M14_S45del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.A5_I35del(1)",
"p.K1454fs*3(1)|p.K1192fs*3(1)|p.?(1)", "p.P542R(1)"), class = "factor")), .Names = c("V1",
"V5", "V6", "V7", "V9", "V10", "V11", "V13", "V14", "V15", "V35",
"V42", "V57"), row.names = c(NA, 4L), class = "data.frame")
我相信您可能会在阅读它们时说跳过几行，以便我可以将它们轻松地添加在一起，因为第三行都是相同的，但是我需要保留前两个标题，我只知道它们为此做
FileName = file.choose()
input = file(FileName, open = "r")
Header = readLines(input, 2)
Data <- read.csv(input)
close(input)
output = file(FileName, open = "w")
writeLines(Header, output)
write.csv(Data, output, row.names = F)
close(output)
我不知道如何在forloop中做到这一点