a question about the use of R package-GenomicFeatures

[masylichu]

Hi,all
i want to use the R biocondunctor package-GenomicFeatures.and i follow the manual to install this package.

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("GenomicFeatures")

it sounds no problem.

however, when i type R and enter the R command,
>library(GenomicFeatures)
>txdb<- makeTranscriptDbFromUCSC(genome='hg19',tablename='ensGene'),

Error: could not find function "makeTranscriptDbFromUCSC"

why?

could someone help me to solve this?

[Zigster]

that's weird
i'll assume the trailing comma and space before ' ensGene' are just typos

what does it say when you type:
> ls("package:GenomicFeatures")

[masylichu]

> ls("package:GenomicFeatures")
[1] "exons" "extractTranscriptsFromGenome"
[3] "introns" "transcripts"

this is the output.

[masylichu]

also, the problem happen after i deleted the space before ' ensGene'.

that's weird
i'll assume the trailing comma and space before ' ensGene' are just typos

what does it say when you type:
> ls("package:GenomicFeatures")

[Zigster]

that comes from an old version of Bioconductor

Install R 2.12.0 then reinstall Bioconductor

[masylichu]

all right. i will have a try.

that comes from an old version of Bioconductor

Install R 2.12.0 then reinstall Bioconductor