IVAS (version 1.4.0)

MsqtlFinder: Find SQTLs in multiple genes.

Description

This function enables one to analyze multiple genes using multi-thread version of the foreach function and joins output results from sqtlfinder function. Moreover, it calculates the FDR using P-values of the matrix result data.

Usage

MsqtlFinder(expdata = NULL, snpdata = NULL, snplocus = NULL, GTFdata = NULL,
met = NULL, Ncor = 1, bplotout = NULL, cutFDR = 0.01)

Arguments

expdata

Dataframe of expression data.

snpdata

Dataframe of genotype data.

snplocus

Locus of SNP markers in the snpdata.

GTFdata

The transcriptDb object in the GnomicFeatures package.

met

The option for statistical models.("lm" : analysis using linear regression model, "glm" : analysis using generalized linear mixed model,and "both" : "lm" and "glm").

Ncor

The number of cores for multi-threads.

bplotout

A directory saving boxplots

cutFDR

The false discovery rate value you would like to set threshold.

Value

This function returns the result matrix including SNP markers ID, chromosome number, alternative exons range, intron ranges, alternative type, P value, information of differential median values of expression ratio among genotypes ("sig" if differential median > 0.1 and "not sig" otherwise), gene names, methods ("lm" or "glm").

References

Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, Morgan M, and Carey V. Software for Computing and Annotating Genomic Ranges. PLoS Computational Biology, 9, e1003118. 2013. Benjamini, Yoav, Hochberg, and Yosef. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, Series B 57, 289-300. 1995.

See Also

foreach, GRanges, p.adjust

Examples

sampleDB <- system.file("extdata", "sampleDB", package="IVAS")
sample.Txdb <- loadDb(sampleDB)
data(sampleexp)
data(samplesnp)
data(samplesnplocus)
#final.result <- MsqtlFinder(sampleexp,samplesnp,samplesnplocus,sample.Txdb,"lm",1)