RDAVIDWebService Package - Uploading a gene list using data()
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hpw9 • 0
@hpw9-7301
Last seen 7.5 years ago
United States

Hi,

I have been using DAVID for a while now, but I am totally new to the DavidWebService package for R.

I load the package and initiate the analysis in a similar way to what is used as an example in the vignette for connectivity basic work flow:

R> library("RDAVIDWebService")
R> david<-DAVIDWebService$new(email="user@inst.org")
R> data(demoList1)
R> result<-addList(david, demoList1,
+ idType="AFFYMETRIX_3PRIME_IVT_ID",
+ listName="demoList1", listType="Gene")
R> result

The problem is the data() command. The above example uses the integrated demoList1 example dataset which contains geneids as a character vector.

I have uploaded a simple csv file containing a list of 2000 gene IDs (corresponding to OFFICIAL_GENE_SYMBOL), which of course loads as a dataframe, which I call 'genelistdavid'. However, when I run

data(genelistdavid)

I receive the following error:

Warning message:
In data(genelistdavid) : data set ‘genelistdavid’ not found

The same thing happens when I create a new character vector from genelistdavid using as.character().

Does anyone have a fix for this failure to load my genelist into the david environment? Thanks so much.

 

rdavidwebservice david differential gene expression annotation • 1.3k views
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 18 months ago
United States

data() reads in a serialized (saved) R object, in this case a character vector. For reading in a csv file, you want to use read.csv().

Enter

?read.csv

to get help on this function. 

Dan

 

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