[BioC] How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?

[Ying Chen]

Sorry, one more question regarding the transcripts argument:

For the following two transcripts:

	uc001aaa.3	chr1:11874-12227,12613-12721,13221-14409:+
	uc010nxq.1	chr1:11874-12227,12595-12721,13403-14409:+

What should be the format for tx_start and tx_end?

transcripts <- data.frame(
		tx_id=c("uc001aaa.3"," uc010nxq.1"),
		tx_chrom="chr1",
		tx_strand="+",
		tx_start=c(11874, 11874),
		tx_end=c(14409, 14409))

or:

transcripts <- data.frame(
		tx_id=c("uc001aaa.3","uc001aaa.3","uc001aaa.3","uc010nxq.1","uc010nxq.1","uc010nxq.1"),
		tx_chrom="chr1",
		tx_strand="+",
		tx_start=c(11874,12613,13221,11874,12595,13403),
		tx_end=c(12227,12721,14409,12227,12721,14409))

Thanks a lot for the help!

Ying

-----Original Message-----
From: bioconductor-bounces at r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Ying Chen
Sent: Tuesday, October 09, 2012 10:57 AM
To: bioconductor at r-project.org
Subject: [BioC] How to set up genes argument for makeTranscriptDb( ) function in GenomicFeatures?

Hi guys,

I am new to the GenomicsFeatures package and I am trying to make my own txdb out of TCGA GAF file using the function makeTranscriptDb(transcripts, splicings,genes) in GenomicsFeatures. The manual says that genes is a data frame containing the genes associated to a set of transcripts. I just wonder what format should it be. Will the following work?

 genes <- data.frame(
                   tx_id=c(txid1,txid2, txid3, txid4, txid5, txid6, txid7, txid8, txid9,............),                                                              # first 9 tx_ids for 3 gene_ids are listed
                  gene_id=c(geneid1, geneid1, geneid2, geneid2, geneid2, geneid3, geneid3, geneid3, geneid3,.......))     # first 3 gene_ids are listed

Thanks a lot for the help!

Ying

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