CalSigSNP: Calculate significance SNPs

In IVAS: Identification of genetic Variants affecting Alternative Splicing

Description

This function performs linear regression test to identify significance associations between expression ratio and genotypes using the lm function.

Usage

    CalSigSNP(ratio.mat=NULL,snp.mat=NULL,overlapsnp=NULL,
        each.snplocus=NULL,chr,each.gene=NULL,GroupSam=NULL,method="lm")

Arguments

ratio.mat	A data frame consisting of expression ratio of an alternatively spliced exon.
snp.mat	A data frame of genotype data.
overlapsnp	A data frame containing SNPs which is within an alternatively spliced exon and its flanking introns.
each.snplocus	A data frame consisting of locus information of SNP markers in the snpdata.
chr	The chromosome number that you would like to test in this function.
each.gene	The gene name that you would like to test in this function
GroupSam	A list object of a group of each sample.
method	The option for statistical models and boxplot.("lm" : analysis using linear regression model, "glm" : analysis using generalized linear mixed model, "both" : "lm" and "glm", and "boxplot" : for writing boxplot).

Value

The lm or glm method returns matrix including; SNP marker IDs, P values, information of differential median values of expression ratio among genotypes ("sig" if differential median > 0.1 and "not sig" otherwise), gene names, and methods ("lm" or "glm"). The boxplot method returns matrix with relative ratio values and genotypes of samples.

Author(s)

Seonggyun Han, Sangsoo Kim

References

Chambers, J. M. (1992) Linear models. Chapter 4 of Statistical Models in S eds J. M. Chambers and T. J. Hastie, Wadsworth & Brooks/Cole.

See Also

lm, glmer

Examples

    sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
    sample.Txdb <- loadDb(sampleDB)
    data(sampleexp)
    data(samplesnp)
    data(samplesnplocus)
    ASdb <- Splicingfinder(sample.Txdb)
    ASdb <- RatioFromFPKM(sample.Txdb,ASdb,sampleexp,CalIndex="ASS7")
    ratio.mat <- slot(ASdb,"Ratio")$ASS
    ratio.mat <- rbind(ratio.mat[,grep("NA",colnames(ratio.mat))])
    each.snp <- rbind(samplesnp[rownames(samplesnp) == "rs3810232",])
    each.snplocus <- rbind(samplesnplocus[samplesnplocus[,"SNP"] == "rs3810232",])
    overlapsnp <- rbind(c(snp="rs3810232",locus="54704760"))
    CalSigSNP(ratio.mat,as.matrix(each.snp),overlapsnp,each.snplocus,"19","ENSG00000170889",method="lm")

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