REIDS (version 0.1.0)

REIDS_Analysis: REIDS_Analysis

Description

The REIDS_Analysis is a wrapper function for the REIDSFunction, the ASExon function, the REIDS_JunctionAssesment function and the REIDS_IsoformAssesment function.

Usage

REIDS_Analysis(geneIDs, Indices, DataFile, nsim = 5000,
  informativeCalls = FALSE, Summarize = TRUE, rho = 0.5,
  Exonthreshold = 0.5, significancelevel = 0.05, Groups, paired = FALSE,
  Low_AllSamples = c(), Low_GSamples = c(), Juninfo = "User",
  JAnnotI = NULL, JAnnot = NULL, EandTrAnnotI = NULL,
  EandTrAnnot = NULL, PartiallyAnnotated = FALSE, positionData = NULL,
  transcriptData = NULL, Location = "Output", Name = "REIDSAnalysis")

Arguments

geneIDs

A vector with the geneIDs to analyze.

Indices

The .csv file created by Line_Indexer.py which contains indices for every gene.

DataFile

The .csv file created by PivotTransformation.

nsim

The number of iterations to perform. Defaults to 1000.

informativeCalls

Logical. Should the I/NI calls method be perform before applying the REIDS model?

Summarize

A character vector specifying the wich summarization method to be performed. The choices are using "EqualAll", "WeightedAll", "EqualConst", "WeightedConst". The former two use all probe sets while the latter to use only the consituitive probe sets. Summarization on the consistuitive probe sets will only be performed if ASPSR is specified.

rho

The threshold for filtering in the I/NI calls method. Probesets with scores higher than rho are kept.

Exonthreshold

The exon score threshold to be maintained. If not NULL, probesets with an exon score lower than this value are not considered further and the p-values will be adjusted for multiplicity after testing. If NULL, all probesets are considered and a multiplicity correction is not performed.

significancelevel

The significance level to be maintained on the p-values. The filtering on the significance is conducted only if an Exonthreshold is specified and the p-value are adjusted for multiplicity.

Groups

A list with elements specifying the columns of the data in each group.

paired

Logical. Are the groups paired? If TRUE the mean paired differences are calculated and tested whether these are significantly different from zero or not.

Low_AllSamples

A character vector containing the probe sets which are not DABG in all samples.

Low_GSamples

A list with a character vector per group containing the probe sets which are not DABG in that group.

Juninfo

A parameter specifying wether the annotations are user of Ensembl defined. If JunInfo is "User" (default) the annotations provided in EandTrAnnot are used. If JunInfo is "Ensembl" the annotations in EandTrAnnot are used to set up tje junction associations but the gene name and position in transcriptData and positionData are used to connect with the Ensembl data base and retrieve corresponding information.

JAnnotI

The file name with line indices for the junction associations.

JAnnot

The file name with the junction associations.

EandTrAnnotI

The file name with line indices for the exon and isoform annotations.

EandTrAnnot

The file name with the exon and isoform annotations.

PartiallyAnnotated

Logical. Should the exon annotations with partially annotated probe sets still be included? If FALSE, these are excluded. If TRUE, these are included. Default is FALSE.

positionData

The file with the chromosome start and ends for the probe sets. Only needed in JunInfo=Ensembl.

transcriptData

The file with gene name of the transcripts. Only needed in JunInfo=Ensembl.

Location

A character string indication the place where the outputs are saved. Defaults to Output.

Name

A character string with the name of the ouput file. Defaults to "REIDSAnalysis".

Value

The output will be written to each of the corresponding .txt files of the called upon functions.

Examples

# NOT RUN {
data(TC1500264)
PivotTransformData(Data=TC1500264,GeneID=NULL,ExonID=NULL,
REMAPSplitFile="TC1500264_Gene_SplitFile.txt",Location="Output/",Name="TC1500264_Pivot")

REIDS_Analysis(Indices="Output/TC1500264_LineIndex.csv",DataFile="Output/TC1500264_Pivot.csv",
nsim=100,informativeCalls=FALSE,Summarize=c("WeightedAll","EqualAll","WeightedConst","EqualConst"),
rho=0.5,Exonthreshold=0.5,significancelevel=0.05,Groups=Groups,paired=FALSE,Low_AllSamples=c()
,Low_GSamples=c(),Juninfo="User",JAnnotI=NULL,JAnnot=NULL,EandTrAnnotI="Output/REMAP_Indices.txt",
EandTrAnnot="Output/HJAY_REMAP.txt",positionData=NULL,transcriptData=NULL,
Location="OutputREIDSAnalysis",Name="TC1500264")
# }