MiRaGE: Inference of Target Gene Regulation via MicroRNA

Description Usage Arguments Details Value References Examples

View source: R/MiRaGE_r.R

Description

Wrapper function computes P-values for target gene regulation via miRNAs.

Usage

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MiRaGE(gene_exp,location="local",species="MM",ID="refseq",method="mean",test="ks",
conv="conserved",species_force=T,ID_force=T,conv_force=T)

Arguments

gene_exp

ExpressionSet object which stores target gene expression. featureData must include "gene_id" and phenoData must include "sample_name". The number of columns of expression data MUST be the length of "sample_name". If not, subsetting is required.

location

Specify from where tables are retrieved. If location="local", then tables are retrieved from experimental package, "miRNATarget". If location="web", tables are downloaded from MiRaGE Server web site, "http://www.granular.com/DATA/". Default is "local"

species

a string specifies target species. This should be either "MM" (mouse) or "HS" (human).Default is "MM".

ID

a string specifies gene ID. Default is "refseq".

method

a string specifies the treatment of samples. This should be one of "mean", "mixed", or "one_by_one". Default is "mean".

test

a string specifies statistical test for P-value computation. This should be one of "ks" (Kolmogorov-Smirnov test), "t" (t-test), or "wilcox" (Wilcoxon test). Default is "ks".

conv

a string specifies conservation of miRNA. This should be one of "conserved", "weak_conserve", and "all". Default is "conserved".

species_force

a boolean indicating whether target gene table is downloaded (TRUE) or not (FALSE). Default is TRUE.

ID_force

a boolean indicating whether gene ID conversion table is downloaded (TRUE) or not (FALSE). Default is TRUE.

conv_force

a boolean indicating whether miRNA conservation table is downloaded (TRUE) or not (FALSE). Default is TRUE.

Details

This wrapper function computes P-values for target gene regulation via miRNAs using the algorithm employed for the MiRaGE server described in Yoshizawa et al (2011). P-values are computed based upon the target gene expression change between two experimental conditions.

Value

P0

data frame. The first column of "P0" contains miRNA names. From the second column to last column includes P-values. Smaller P-values mean that target genes are more likely upregulated in the later sample groups than in the former sample groups

P1

data frame. The first column of "P1" contains miRNA names. From the second column to last column includes P-values. Smaller P-values mean that target genes are more likely downregulated in the later sample groups than in the former sample groups

References

Yoshizawa, M., Taguchi, Y-h., and Yasuda, J. (2011), Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method. Int J Mol Sci 12(12):9265-9276

Examples

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data(gene_exp)
result <- MiRaGE(gene_exp,species="HS")
result$P1[1:3,]

Bioconductor-mirror/MiRaGE documentation built on May 29, 2017, 8:30 a.m.