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Internal function to compute row sums of a matrix.
● Data Source:
CranContrib
● Keywords:
● Alias: rowsumscpp
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Internal function that computes p-values from our joint score test
● Data Source:
CranContrib
● Keywords:
● Alias: jag_fun
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Internal function that computes p-values from our joint score test.
● Data Source:
CranContrib
● Keywords:
● Alias: jagSIM
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Function to 1) create sub-directories, 2) slice gene expression data into partitions of predetermined size, and 3) sliced gene expression partitions are deposited into each sub-directory
● Data Source:
CranContrib
● Keywords: gene expression, partition, slice, sub-directory
● Alias: jaguar_slice
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Internal function to perform cis-eQTL analysis
● Data Source:
CranContrib
● Keywords:
● Alias: cis_eqtl
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The aim of the package is allow users to apply a novel score test method developed to map eQTL in the presence of multiple correlated groups (for example, tissues) from the same individual. We plan to do this by jointly analyzing all the groups by simultaneously measuring the total shift in the gene expression data due to genotypes and group-specific interaction of the genotypes with the gene expression data. Here is an example of a workflow.
● Data Source:
CranContrib
● Keywords:
● Alias: JAGUAR-package
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jaguar_example
(Package: JAGUAR) :
Simulated multi-tissue eQTL data
This is a list object containing a simulated eQTL data
● Data Source:
CranContrib
● Keywords: eQTL, eQTL dataset
● Alias: jaguar_example
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Function to run power/null simulations by simulating one gene and one SNP at a time. The objective of these simulations is two pronged - 1) Check for the type I error control for the joint score test statistic, and 2) Compare two different null hypotheses where one's called a global null (bta=0 and PVEg =0) and other is local null (PVEg=0). Under the global null hypotheses, we fit a model where we assume that there is no main genotypic effect and group-specific variability in the data. Under the local null, we fit a model where we assume only the absence of group-specific variability. This is essentially a variance component score test.
● Data Source:
CranContrib
● Keywords: GWAS, eQTL, score test, simulations
● Alias: jaguar_sim
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Internal function that computes the joint score test statistic over all the SNPs for all the genes
● Data Source:
CranContrib
● Keywords:
● Alias: GENEapply
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Function that processes results from running a genome-wide analysis of jaguar and outputs gene-SNP pairs deemed significant by using a predetermined threshold value. It also has an option to print QQ-plot of the p-values from the analysis.
● Data Source:
CranContrib
● Keywords: GWAS, eQTL, score test
● Alias: jaguar_process
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providing 
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