[BioC] annaffy - saveHTML changed behaviour in newer versions

[Paul Leo]

Thanks Colin, 

That would be great! I tried one other test also after my email. I
loaded the old version of annaffy that worked under R2.5 into R2.7. The
same "bad" behaviour resulted. I suspected the problems came from the
merge commands .... Which is probably less commonly used with annaffy...
However my tested included using exactly the same data_table object in
both R versions just before using the saveHTML command (saved workspace
under R2.5 loaded into R2.7 and just the saveHTML was run : same
effect). Hope that info is of some use...

 

Attached is the output.

 

 

Anyway here is the guts:

 

THE INPUT is the table "top":

> top

                CHR         US         UK      UK_US      posn

RS785702    5  6.173e-03 3.217e-253  4.628e-03 122480032

RS258415   12         NA 1.109e-199         NA  27908789

RS7006137   8 9.323e-119 4.770e-197 5.180e-205 132952261

 

> rownames(top)

[1] "RS785702"  "RS258415"  "RS7006137"

> colnames(top)

[1] "CHR"   "US"    "UK"    "UK_US" "posn"

 

 

R COMMANDS:

library(annaffy)

############ a table

filename<- "topUK50.html"

title <- "Top 50 in UK : with UK+US and US for comparison "

 

newURLs<-lapply(sub("RS","",rownames(top)),function(x) paste('<a
href="http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=',x,'">', sep = "",
collapse = NULL) )

newURLs<-paste(newURLs,rownames(top),sep="",collapse=NULL)

newURLs<-unlist(newURLs)

acc_table<-aafTable("SNP",items=list(newURLs),colnames="SNP") #tried
diff versions of this line but it didn't work..

 

 

chr_table <-aafTable("Chr"=as.character(top[,"CHR"]))

loc_table <-aafTable("Posn"=as.character(top[,"posn"]))

UK_table <-aafTable("UK"=signif(as.numeric(top[,"UK"]),3 ))

UK_US_table<- aafTable("UK_US"=signif(as.numeric(top[,"UK_US"]),3 ))

US_table<- aafTable("US"=signif(as.numeric(top[,"US"]),3 ))

 

data_table <- merge(acc_table,chr_table)

data_table <- merge(data_table,loc_table)

data_table <- merge(data_table,UK_table)

data_table <- merge(data_table,UK_US_table)

data_table <- merge(data_table,US_table)

saveHTML(data_table,filename,title)

 

 

Cheers

Paul

 

PS sessionInfo() provided in the first email of this thread

 

Cheers

Paul

 

 

________________________________

From: Colin A. Smith [mailto:colin at colinsmith.org] 
Sent: Tuesday, 9 October 2007 3:58 AM
To: bioconductor at stat.math.ethz.ch
Cc: Paul Leo
Subject: Re: [BioC] annaffy - saveHTML changed behaviour in newer
versions



Paul-



R 2.6.0 is a lot more picky about the kinds of R variables for which it
will do S4 methods dispatch. To be able to figure out the problem, I
need to see the exact sequence of commands you used to generate the
aafTable object. 



-Colin



On Oct 8, 2007, at 3:00 , bioconductor-request at stat.math.ethz.ch wrote:





Date: Mon, 8 Oct 2007 11:18:07 +1000

From: "Paul Leo" <p.leo at uq.edu.au>

Subject: [BioC] annaffy - saveHTML changed behaviour in newer versions

To: <bioconductor at stat.math.ethz.ch>

Message-ID:

                <
DE3D1F203DAF7A4CB259560D2801DF8B0166BB44 at UQEXMB2.soe.uq.edu.au>

Content-Type: text/plain



HI



I use annaffy to make nice HTML tables of various forms of data, but

save "saveHTML" has changed and the wheels have fallen off. I'm not sure

is the authors intended the change in functionality or not?

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