[BioC] readFASTA Arguments

[Martin Morgan]

Colleen Doherty <colleen.doherty at gmail.com> writes:

> Hi,
>  I am trying to use readFASTA in Biostrings.
>
> As this it works fine:
> Tair8upstream<-readFASTA("TAIR8_upstream_500_20080228",strip.descs=FALSE)
>
> I would like to use some of the other arguments - use.descs, width,
> and checkComments
> However, I get an error when I try this.
>
>> Tair8upstream<-readFASTA("TAIR8_upstream_500_20080228",strip.descs=FALSE, use.descs=TRUE)
> Error in readFASTA("TAIR8_upstream_500_20080228", strip.descs = FALSE,  :
>   unused argument(s) (use.descs = TRUE)

Hi Colleen --

If I do

> ?readFASTA

I see in the usage section


       fasta.info(file, use.descs=TRUE)
       readFASTA(file, checkComments=TRUE, strip.descs=TRUE)
       writeFASTA(x, file="", width=80)

use.descs and width are arguments to other functions described on this
page, not to readFASTA. Perhaps that is the source of your confusion?
Do the arguments provide functionality that is not otherwise
available?

Martin

> or
>
>> Tair8upstream<-readFASTA("TAIR8_upstream_500_20080228",strip.descs=FALSE, width = 250)
> Error in readFASTA("TAIR8_upstream_500_20080228", strip.descs = FALSE,  :
>   unused argument(s) (width = 250)
>
> I didn't see an example with these arguments in the manual, so maybe I
> do not have the correct format.
> Any suggestions?
>
> sessionInfo is below.
>
> Thanks,
> Colleen
>
>
>> sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-04-22 r48368)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Biostrings_2.13.5 IRanges_1.3.8
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.5.0
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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