readFASTA Arguments
1
0
Entering edit mode
@colleen-doherty-2411
Last seen 9.6 years ago
Hi, I am trying to use readFASTA in Biostrings. As this it works fine: Tair8upstream<-readFASTA("TAIR8_upstream_500_20080228",strip.descs=FAL SE) 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=F ALSE, use.descs=TRUE) Error in readFASTA("TAIR8_upstream_500_20080228", strip.descs = FALSE, : unused argument(s) (use.descs = TRUE) or > Tair8upstream<-readFASTA("TAIR8_upstream_500_20080228",strip.descs=F ALSE, 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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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
Biostrings Biostrings • 864 views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 6 weeks ago
United States
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=F ALSE) > > 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_IDEN TIFICATION=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD COMMENT

Login before adding your answer.

Traffic: 862 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6