[BioC] regarding makeTranscriptDbFromGFF

[James W. MacDonald]

Hi Deepika,

On Wednesday, September 25, 2013 9:44:48 AM, deepika lakhwani wrote:
> Hello
>
> I apologize for bothering you again. I wanted to use

You aren't necessarily bothering anybody, but you certainly aren't 
helping either us or yourself. You should ALWAYS include the output of 
sessionInfo() when you send a question, because that will show us what 
you actually did, rather than what you said you did. It will also let 
us know which version of R/BioC you are using.

As an example, you say you loaded the Genomicfeatures (sic) package. 
Since there is no such package, it is not unexpected that you would not 
be able to find the function you seek. I have no such problem when I 
load GenomicFeatures:

> library(GenomicFeatures)
> makeTranscriptDbFromGFF
function (file, format = c("gff3", "gtf"), exonRankAttributeName = NULL,
    gffGeneIdAttributeName = NULL, chrominfo = NULL, dataSource = NA,
    species = NA, circ_seqs = DEFAULT_CIRC_SEQS, miRBaseBuild = NA)
{
    format <- match.arg(format)
    feature.type <- c("gene", "mRNA", "exon", "CDS")
    gff <- import(file, format = format, feature.type = feature.type,
        asRangedData = FALSE)
    if (format == "gff3") {
        if (all(c("ID", "Parent") %in% colnames(mcols(gff)))) {
            tables <- .prepareGFF3Tables(gff, exonRankAttributeName,
                gffGeneIdAttributeName)
        }
    }
    else if (format == "gtf") {
        if (all(c("gene_id", "transcript_id") %in% 
colnames(mcols(gff)))) {
            tables <- .prepareGTFTables(gff, exonRankAttributeName)
        }
    }
    metadata <- .prepareGFFMetadata(file, dataSource, species,
        miRBaseBuild)
    if (is.null(chrominfo)) {
        message("Now generating chrominfo from available sequence 
names. No chromosome length information is available.")
        chroms <- unique(tables[["transcripts"]][["tx_chrom"]])
        chrominfo <- data.frame(chrom = chroms, length = rep(NA,
            length(chroms)), is_circular = matchCircularity(chroms,
            circ_seqs))
    }
    txdb <- makeTranscriptDb(transcripts = tables[["transcripts"]],
        splicings = tables[["splicings"]], genes = tables[["genes"]],
        chrominfo = chrominfo, metadata = metadata, reassign.ids = TRUE)
    txdb
}
<environment: namespace:GenomicFeatures>
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6   Biobase_2.20.1
[4] GenomicRanges_1.12.5   IRanges_1.18.3         BiocGenerics_0.6.0

loaded via a namespace (and not attached):
 [1] biomaRt_2.16.0     Biostrings_2.28.0  bitops_1.0-6       
BSgenome_1.28.0
 [5] DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.12.4   
RSQLite_0.11.4
 [9] rtracklayer_1.20.4 stats4_3.0.1       tools_3.0.1        
XML_3.98-1.1
[13] zlibbioc_1.6.0

Best,

Jim


> makeTranscriptDbFromGFF function but after loading the Genomicfeatures
> package and run makeTranscriptDbFromGFF(). I got error
>
> Error: could not find function "makeTranscriptDbFromGFF"
>
> I do not know that What am I doing wrong.
>
>
> I ran:
>> txdb <-makeTranscriptDbFromGFF(file = 'mm9.gtf', format =
> "gtf",exonRankAttributeName = "exon_number", chrominfo = chrominfo,
> dataSource = "UCSC", species = "Mus musculus")
> Error: could not find function "makeTranscriptDbFromGFF"
>
> then i ran
>
> makeTranscriptDbFromGFF()
> Error: could not find function "makeTranscriptDbFromGFF"
>
>
> please resolve my problem.
>
>
>
> thanking you
>
>
> regards
> deepika
>
> 	[[alternative HTML version deleted]]
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099