The matrix of transcripts including transcript IDs, Ensembl gene names, Ensembl transcript names, transcript start sites, and transcript end sites.
total.locus
Ranges including alternative exons and flanking introns in a gene.
exon.locus
All exon locus of a single gene.
intron.locus
All intron locus of a single gene.
info.strand
The strand informatrion of a single gene (forward strand = "+", reverse strand = "-").
overapvalue
Snps located in the alternative exons and the flanking introns
chrnum
The chromosome number of a single gene.
expdata
Dataframe of expression data.
snpdata
Datafame of genotype data.
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, Chromosome numbers, alternative exons ranges, Intron rangess, alternative types, 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.
Breslow, N.E. Clayton, D.G. (1993). Approximate Inference in Generalized Linear Mixed Models. Journal of the American Statistical Association 88.