[BioC] PostForm and readHTML Table

[Ovokeraye Achinike-Oduaran]

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 passingÂ
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] 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
>