Hi all, 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. Thanks. -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 11q14.32q31.17p132q31.17p21.211q14.32p23.32p23.33q21.12p23.311p11.27p2 1.27p1310q25.211q12.211p11.29p24.211q12.23q26.29p24.23q21.11q32.38q24. 1112q23.210q25.212q23.215q22.210q25.21q32.33q26.2\r\n MTNR1BG6PC2GCKG6PC2DGKB, TMEM195MTNR1BGCKRGCKRADCY5GCKRMADDDGKB, TMEM195GCKADRA2AFADS1CRY2GLIS3FADS1SLC2A2GLIS3ADCY5PROX1SLC30A8IGF1TCF 7L2IGF1C2CD4BADRA2APROX1SLC2A2\r\n \r\n\t\tMTNR1BG6PC2GCK - YKT6G6PC2EEF1A1P26 - TMEM195MTNR1BGCKRGCKRADCY5GCKRMADDEEF1A1P26 - TMEM195GCK - YKT6ADRA2A - RPS6P15FADS1CRY2GLIS3FADS1SLC2A2GLIS3ADCY5RPL31P13 - PROX1SLC30A8IGF1TCF7L2IGF1C2CD4A - C2CD4BADRA2A - RPS6P15RPL31P13 - PROX1SLC2A2\r\n rs10830963-Grs560887-Crs4607517-Ars560887-Crs2191349-Trs10830963-Grs78 0094-Crs780094-Crs11708067-Ars780094-Crs7944584-Ars2191349-Trs4607517- Ars10885122-Grs174550-Trs11605924-Ars7034200-Ars174550-Trs11920090-Trs 7034200-Ars11708067-Ars340874-Crs11558471-Ars35767-Grs4506565-Trs35767 -Grs11071657-Ars10885122-Grs340874-Crs11920090-T\r\n\t\tintronintronin tergenicintronintergenicintronintronintronintronintronintronintergenic intergenicintergenicintronintronintronintronintronintronintronintergen icUTR-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] LC_COLLATE=English_xxx LC_CTYPE=English_xxx [3] LC_MONETARY=English_xxx LC_NUMERIC=C [5] LC_TIME=English_xxx attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RHTMLForms_0.5-1 XML_3.4-2.2 RCurl_1.6-10.1 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] tools_2.13.2 >

On 10/17/2011 08:47 AM, Ovokeraye Achinike-Oduaran wrote: > Hi all, > > 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. > > Thanks. > > -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 I think you are after table 6, but you will still have problems with screen scraping. Maybe more straight-forward to download the tab-delimited file of the entire data base, offered on that page? Martin > >> 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 > 11q14.32q31.17p132q31.17p21.211q14.32p23.32p23.33q21.12p23.311p11.27 p21.27p1310q25.211q12.211p11.29p24.211q12.23q26.29p24.23q21.11q32.38q2 4.1112q23.210q25.212q23.215q22.210q25.21q32.33q26.2\r\n > MTNR1BG6PC2GCKG6PC2DGKB, > TMEM195MTNR1BGCKRGCKRADCY5GCKRMADDDGKB, > TMEM195GCKADRA2AFADS1CRY2GLIS3FADS1SLC2A2GLIS3ADCY5PROX1SLC30A8IGF1T CF7L2IGF1C2CD4BADRA2APROX1SLC2A2\r\n > \r\n\t\tMTNR1BG6PC2GCK - YKT6G6PC2EEF1A1P26 - > TMEM195MTNR1BGCKRGCKRADCY5GCKRMADDEEF1A1P26 - TMEM195GCK - YKT6ADRA2A > - RPS6P15FADS1CRY2GLIS3FADS1SLC2A2GLIS3ADCY5RPL31P13 - > PROX1SLC30A8IGF1TCF7L2IGF1C2CD4A - C2CD4BADRA2A - RPS6P15RPL31P13 - > PROX1SLC2A2\r\n > rs10830963-Grs560887-Crs4607517-Ars560887-Crs2191349-Trs10830963-Grs 780094-Crs780094-Crs11708067-Ars780094-Crs7944584-Ars2191349-Trs460751 7-Ars10885122-Grs174550-Trs11605924-Ars7034200-Ars174550-Trs11920090-T rs7034200-Ars11708067-Ars340874-Crs11558471-Ars35767-Grs4506565-Trs357 67-Grs11071657-Ars10885122-Grs340874-Crs11920090-T\r\n\t\tintronintron intergenicintronintergenicintronintronintronintronintronintronintergen icintergenicintergenicintronintronintronintronintronintronintroninterg enicUTR-3nearGene-5intronnearGene- 5intergenicintergenicintergenicintron\r\n > \r\n > \r\n\t\t0.300.700.160.700.520.300.620.620.780.620.750.520.160.870.64 0.490.490.640.870.490.780.520.310.850.310.850.630.870.520.87\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] LC_COLLATE=English_xxx LC_CTYPE=English_xxx > [3] LC_MONETARY=English_xxx LC_NUMERIC=C > [5] LC_TIME=English_xxx > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RHTMLForms_0.5-1 XML_3.4-2.2 RCurl_1.6-10.1 bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] tools_2.13.2 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793