RatioFromFPKM: Estimate relative expression ratio.

In IVAS: Identification of genetic Variants affecting Alternative Splicing

Description

With the FPKM expression data set of transcripts, this function estimates relative expression ratio between transcripts with and without alternatively spliced exons based on splicing models of the ASdb object

Usage

    RatioFromFPKM(GTFdb = NULL, ASdb = NULL, 
        Total.expdata = NULL, CalIndex = NULL, Ncor = 1, out.dir = NULL)

Arguments

GTFdb	A TxDb object in the GenomicFeatures package.
ASdb	A ASdb object including "SplicingModel" slot from the Splicingfinder function.
Total.expdata	A data frame of expression data.
CalIndex	An index number in the ASdb object which will be tested in this function.
Ncor	The number of cores for multi-threads function.
out.dir	An output directory.

Value

ASdb with the slot (labeled by "Ratio") containing results from the the RatioFromFPKM function. The "Ratio" slot contains a list object and each element of the list object returns the results assigned to three elements, which is of each alternative splicing type (i.e. Exon skipping, Alternative splice site, Intron retention). Three elements are as follows;

ES	A data frame for the result of Exon skipping, consisting of the columns named as follows; Index (index number), EnsID (gene name), Nchr (chromosome name), 1stEX (alternatively spliced target exon), 2ndEX (second alternatively spliced target exon which is the other one of the mutually exclusive spliced exons), DownEX (downstream exon range), UpEX (upstream exon range), Types (splicing type), and names of individuals.
ASS	A data frame for the result of Alternative splice sites, consisting of the columns named as follows; Index (index number), EnsID (gene name), Nchr (chromosome name), ShortEX (shorter spliced target exon), LongEX (longer spliced target exon), NeighborEX (neighboring down or upstream exons), Types (splicing type), and names of individuals.
IR	A data frame for the result of Intron retention, consisting of the columns named as follows; Index (index number), EnsID (gene name), Nchr (chromosome name), RetainEX (retained intron exon), DownEX (downstream exon range), UpEX (upstream exon range), Types (splicing type), and names of individuals.

Author(s)

Seonggyun Han, Sangsoo Kim

See Also

isActiveSeq, seqinfo, Splicingfinder

Examples

    sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
    sample.Txdb <- loadDb(sampleDB)
    data(sampleexp)
    ASdb <- Splicingfinder(sample.Txdb)
    ASdb <- RatioFromFPKM(sample.Txdb,ASdb,sampleexp)

IVAS documentation built on Nov. 8, 2020, 5:52 p.m.