assemble.data {SIM}R Documentation

Assemble the data to run the integrated analysis

Description

Assembles the copy number and expression data and annotation.

Usage

assemble.data(dep.data = acgh.data, indep.data = expr.data, ann.dep = colnames(acgh.data)[1:4], ann.indep = colnames(expr.data)[1:4], dep.id = "ID", dep.chr = "CHROMOSOME", dep.pos = "STARTPOS", dep.symb = FALSE, indep.id = "ID", indep.chr = "CHROMOSOME", indep.pos = "STARTPOS", indep.symb = FALSE, overwrite = FALSE, run.name = NULL)

Arguments

dep.data data.frame. The dependent data, along with annotations. Each row should correspond to one feature. The following columns are expected to exist, and the column names should be inserted in the function. dep.id.: A unique identifier. dep.chr.: The number of the chromosome (chrX=23 and chrY=24). dep.pos.: The base pair position, relative to the chromosome. dep.symb.: Gene symbol (optional). The data will be sorted on Abs.start, generated by chr*10e9+basepair.
indep.data data.frame. The independent data, along with annotations. Each row should correspond to one feature. The following columns are expected to exist, and the column names should be inserted in the function. indep.id.: A unique identifier. indep.chr.: The number of the chromosome (chrX=23 and chrY=24). indep.pos.: The base pair position, relative to the chromosome. indep.symb.: Gene symbol (optional). The data will be sorted on Abs.start, generated by chr*10e9+basepair.
ann.dep vector with either the names of the columns or the column numbers in the dependent data that contain the annotation.
ann.indep vector with either the names of the columns or the column numbers in the independent data that contain the annotation.
dep.id vector with the column name in the dependent data that contains the ID. Will be used in the sim.plot.zscore.heatmap function. Empty ID's will be substituted by NA.
dep.chr vector with column name in the dependent data that contains the chromosome numbers.
dep.pos vector with the column name in the dependent data that contains the position on the chromosome in bases.
dep.symb Optional, either F(alse) or a single vector with the column name in the dependent data that contains the Symbols. Will be used in sim.plot.zscore.heatmap as label.
indep.id vector with the column name in the independent data that contains the ID. Will be used in the sim.plot.zscore.heatmap function. Empty ID's will be substituted by NA.
indep.chr vector with the column name in the independent data that contains the chromosome numbers.
indep.pos vector with the column name in the independent data that contains the position on the chromosome in bases.
indep.symb Optional, either F(alse) or a vector with the column name in the dependent data that contains the Symbols. Will be used in sim.plot.zscore.heatmap as label.
overwrite Boolean, indicate when a run.name is already present, the results can be overwritten.
run.name Name of the analysis. The results will be stored in a folder with this name in the current working directory (use getwd() to print the current working directory). If the run.name = NULL, the default folder "analysis_results" will be generated.

Value

No values are returned. Instead, the datasets and annotation columns are stored in seperate files in the data folder in the directory specified in run.name. If the assemble.data function has run succesfully, the integrated.analysis function can be performed.

Author(s)

Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl

See Also

SIM, integrated.analysis, sim.plot.zscore.heatmap, sim.plot.pvals.on.region, sim.plot.pvals.on.genome, tabulate.pvals, tabulate.top.dep.features, tabulate.top.indep.features, impute.nas.by.surrounding, sim.update.chrom.table

Examples

#load the datasets and the samples to run the integrated analysis
data(expr.data)
data(acgh.data)
data(samples) 
         
#read the data
assemble.data(dep.data = acgh.data, indep.data = expr.data, ann.dep = colnames(acgh.data)[1:4], ann.indep = colnames(expr.data)[1:4], dep.id="ID", dep.chr = "CHROMOSOME",dep.pos = "STARTPOS",dep.symb="Symbol", indep.id="ID",indep.chr = "CHROMOSOME", indep.pos = "STARTPOS", indep.symb="Symbol", overwrite = TRUE,run.name ="chr8")

[Package SIM version 1.10.0 Index]