Go Back   SEQanswers > Sequencing Technologies/Companies > MGISEQ (FKA Complete Genomics)

Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: easyRNASeq: a bioconductor package for processing RNA-Seq data. Newsbot! Literature Watch 0 08-01-2012 03:00 AM
how to use medpolish in R/Bioconductor shuang Bioinformatics 1 05-08-2012 08:41 AM
PubMed: HTSanalyzeR: an R/Bioconductor package for integrated network analysis of hig Newsbot! Literature Watch 0 06-01-2011 03:00 AM
ChIP-Seq: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip dat Newsbot! Literature Watch 0 05-13-2010 03:00 AM
ShortRead: a bioconductor package for input, quality assessment and exploration Chien-Yuan Chen Literature Watch 0 11-09-2009 02:36 PM

Thread Tools
Old 10-15-2012, 10:55 AM   #1
Junior Member
Location: USA

Join Date: Oct 2012
Posts: 5
Default Bioconductor package -GADEM

Hello Everyone
I am new to R, and I am trying to use the bioconductor package rGADEM to do de nova motif analysis -
I would like to know what these commands do -

> pwd <- ""
> path <- system.file("extdata/Test_100.fasta", package = "rGADEM")
> FastaFile <- paste(pwd, path, sep = "")
> Sequences <- read.DNAStringSet(FastaFile, "fasta")

I am getting error messages when I run the last command , understanding the commands would help me overcome the frustration.

The error message I got was
(Call2("new_input_ExternalFilePtr", fp, PACKAGE = "Biostrings") :
cannot open file ''
In addition: Warning message:
'read.DNAStringSet' is deprecated.
Use 'readDNAStringSet' instead.
See help("Deprecated")

DNASpeaks is offline   Reply With Quote
Old 06-04-2013, 07:52 AM   #2
Junior Member
Location: Lisbon, Portugal

Join Date: Aug 2012
Posts: 2

error message means you have to install the Biostrings package, which contains several functions including the one missing "readDNAStringSet" (and it's telling you that "read.DNAStringSet" is no longer used).
araposo is offline   Reply With Quote

bioconductor, gadem, motif

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 12:16 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO