Question: (Closed) Using Postform() And Readhtmltable()
0
gravatar for Avoks
7.9 years ago by
Avoks140
Avoks140 wrote:

Hi all,

I posted this question a while ago in the BioC mailing list but didn't quite get a response. So, I'm hoping I get some feedback on here. Here goes:

I ran a query using postForm(), got my results that are supposed to have headers. But when I use header=TRUE in the readHTMLTable function I get an error. Without specifying any parameter for the header, I get the result but it's very hard to read. Is it possible to get this in a readable table form with headers? Any help will be greatly appreciated.

Regards,

Avoks

> data = postForm("http://www.genome.gov/GWAStudies/",
+ multidisease = c("Fasting glucose-related traits"),
+ submit = "Search")

> tbl = readHTMLTable(htmlParse(data, asText = TRUE), which = 5, header = TRUE)

Error in seq.default(length = max(numEls)) : length must be non-negative number In addition: Warning message: In max(numEls) : no non-missing arguments to max; returning -Inf

> tbl = readHTMLTable(htmlParse(data, asText = TRUE), which = 5)
>tbl 

                                                                                                 V1

1 Date Added to Catalog (since 11/25/08)\r\n\r\n First Author/Date/ Journal/Study\r\n\t\t\r\n Disease/Trait\r\n\t\t\r\n InitialSample Size\r\n\t\t\r\n Replication Sample Size\r\n\r\n Region\r\n\t\t\r\n Reported Gene(s)\r\n Mapped Gene(s)\r\n Strongest SNP-Risk Allele\r\n Context\r\n\t\t\r\n Risk Allele Frequency in Controls\r\n P-value\r\n\t\t\r\n OR or beta-coefficient and [95% CI]\r\n\r\n Platform[SNPs passing QC]\r\n CNV\r\n\t\t\r\n\t\t\r\n\t \r\n\t\t\r\n\t\t02/28/10\r\n \r\n\t\t\tDupuis JJanuary 17, 2010Nat GenetNew genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.\r\n\t\t\t\r\n Fasting glucose-related traits\r\n up to 46,186 European descent individuals\r\n up to 76,558 European ancestry individuals\r\n\r\n 11q14.32q31.17p132q31.17p21.211q14.32p23.32p23.33q21.12p23.311p11.27p21.27p1310q25.211q12.211p11.29p24.211q12.23q26.29p24.23q21.11q32.38q24.1112q23.210q25.212q23.215q22.210q25.21q32.33q26.2\r\n MTNR1BG6PC2GCKG6PC2DGKB, TMEM195MTNR1BGCKRGCKRADCY5GCKRMADDDGKB, TMEM195GCKADRA2AFADS1CRY2GLIS3FADS1SLC2A2GLIS3ADCY5PROX1SLC30A8IGF1TCF7L2IGF1C2CD4BADRA2APROX1SLC2A2\r\n \r\n\t\tMTNR1BG6PC2GCK - YKT6G6PC2EEF1A1P26 - TMEM195MTNR1BGCKRGCKRADCY5GCKRMADDEEF1A1P26 - TMEM195GCK - YKT6ADRA2A - RPS6P15FADS1CRY2GLIS3FADS1SLC2A2GLIS3ADCY5RPL31P13 - PROX1SLC30A8IGF1TCF7L2IGF1C2CD4A - C2CD4BADRA2A - RPS6P15RPL31P13 - PROX1SLC2A2\r\n rs10830963-Grs560887-Crs4607517-Ars560887-Crs2191349-Trs10830963-Grs780094-Crs780094-Crs11708067-Ars780094-Crs7944584-Ars2191349-Trs4607517-Ars10885122-Grs174550-Trs11605924-Ars7034200-Ars174550-Trs11920090-Trs7034200-Ars11708067-Ars340874-Crs11558471-Ars35767-Grs4506565-Trs35767-Grs11071657-Ars10885122-Grs340874-Crs11920090-T\r\n\t\tintronintronintergenicintronintergenicintronintronintronintronintronintronintergenicintergenicintergenicintronintronintronintronintronintronintronintergenicUTR-3nearGene-5intronnearGene-5intergenicintergenicintergenicintron\r\n \r\n \r\n\t\t0.300.700.160.700.520.300.620.620.780.620.750.520.160.870.640.490.490.640.870.490.780.520.310.850.310.850.630.870.520.87\r\n 6 x 10-175 (FPG)9 x 10-218 (FPG)7 x 10-92 (FPG)2 x 10-66 (HOMA-B)3 x 10-44 (FPG)3 x 10-43 (HOMA-B)6 x 10-38 (FPG)3 x 10-24 (HOMA-IR)7 x 10-22 (FPG)4 x 10-20 (FI)2 x 10-18 (FPG)3 x 10-17 (HOMA-B)2 x 10-16 (HOMA-B)3 x 10-16 (FPG)2 x 10-15 (FPG)1 x 10-14 (FPG)1 x 10-13 (HOMA-B)5 x 10-13 (HOMA-B)8 x 10-13 (FPG)1 x 10-12 (FPG)3 x 10-12 (HOMA-B)7 x 10-12 (FPG)3 x 10-11 (FPG)2 x 10-9 (HOMA-IR)1 x 10-8 (FPG)3 x 10-8 (FI)4 x 10-8 (FPG)2 x 10-6 (HOMA-B)5 x 10-6 (HOMA-B)5 x 10-6 (HOMA-B)\r\n \r\n NRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNRNR\r\n \r\n\r\n Affymetrix & Illumina [~2.5 million] (imputed)\r\n\t\tN

> sessionInfo()

R version 2.13.2 (2011-09-30) Platform: i386-pc-mingw32/i386 (32-bit)

locale: [1] LCCOLLATE=Englishxxx LCCTYPE=Englishxxx [3] LCMONETARY=Englishxxx LCNUMERIC=C [5] LCTIME=English_xxx

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] RHTMLForms0.5-1 XML3.4-2.2 RCurl1.6-10.1 bitops1.0-4.1

loaded via a namespace (and not attached): [1] tools_2.13.2 >

• 2.7k views
ADD COMMENTlink modified 7.9 years ago by Istvan Albert ♦♦ 81k • written 7.9 years ago by Avoks140
1

this is not a bioinformatics questions but a bioconductor specif problem. If people on the bioconductor list cannot answer it I doubt anyone here knows the answer.

ADD REPLYlink written 7.9 years ago by Istvan Albert ♦♦ 81k
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