MsReport: Produce report for a microRNA (abbreviated miRNA) set

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/MsReport.R

Description

The miR.report includes miRNA names, locstion, S2N, RES and whether is core-enrichment miRNA,

Usage

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MsReport(MsNAME = "", input.ds, input.cls, p_value,
p2miR,weighted.score.type = 1)

Arguments

MsNAME

An interesting pathway name

input.ds

Input miRNA expression Affymetrix dataset file in RES or GCT format

input.cls

Input class vector (phenotype) file in CLS format

p_value

A weighting matrix of p value of the hypergeometric. (rows are pathway ,cols are microRNAs(miRNAs))

p2miR

pathway-miRNA correlation(pmSET) profile

weighted.score.type

Enrichment correlation-based weighting: 0=no weight (KS), 1=standard weigth, 2 = over-weigth (default: 1)

Details

When users input a interesting pathway,the function MsReport can create a report for a miRNA set that coordinated regulate this pathway. MiR : the name of miRNAs. For example the probe accession number, miRNA symbol or the miRNA identifier in the dataset. LIST LOC : location of the miRNA in the sorted miRNA list. S2N : correlation(tw-score) of the miRNA in the miRNA list. RES : value of the running enrichment score at the miRNA location. CORE_ENRICHMENT:whether this miRNA is the "core enrichment" section of the list, Yes or No variable specifying in the miRNA location is before (positive ES) or after (negative ES) the running enrichment peak.

Value

A list. It includes two elements: Msreport and miRList.

Msreport is matrix of input pathway which present the detail results . Its columns include "miRNA name", "location of the miRNA in the sorted miRNA list", "tw-scoe of miRNA", "Running enrichment score", "Property of contribution".

miRList is a list of drawing parameters for function PlotHeatMap,PlotCorrelation and PlotRunEnrichment.

Author(s)

Junwei Han[email protected],Siyao Liu [email protected]

See Also

MirSEA,S2N,EnrichmentScore,PlotHeatMap,PlotCorrelation,PlotRunEnrichment

Examples

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## Not run: 
#get example data
#input.ds <- readLines("F:/lsy/xin data/GSE36915.gct")
#input.cls <- readLines("F:/lsy/xin data/GSE36915.cls")
input.ds <- GetExampleData("dataset")
input.cls <- GetExampleData("class.labels")
 
#get example of p value matrix
p_value <- GetExampleData("p_value")
#get example of correlation profile
p2miR <- GetExampleData("p2miR")

#get a miRNA.SET report for KEGG ERBB PATHWAY
Results<-MsReport(MsNAME = "KEGG_ERBB_SIGNALING_PATHWAY", input.ds, input.cls,p_value,p2miR)
# show the report of top five miRNA in the pathway
Results[[1]][1:5,]

## End(Not run)

MiRSEA documentation built on May 29, 2017, 2:58 p.m.