assemble.data {SIM} | R Documentation |
Assembles the dependent and independent data and annotation of the both data sets.
assemble.data(dep.data, indep.data, dep.id = "ID", dep.chr = "CHROMOSOME", dep.pos = "STARTPOS", dep.ann = NULL, dep.symb, indep.id = "ID", indep.chr = "CHROMOSOME", indep.pos = "STARTPOS", indep.ann = NULL, indep.symb, overwrite = FALSE, run.name = "analysis_results")
dep.data |
The dependent data ( |
indep.data |
|
dep.ann |
|
indep.ann |
|
dep.id |
|
dep.chr |
|
dep.pos |
|
dep.symb |
Optional, either missing 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 |
|
indep.chr |
|
indep.pos |
|
indep.symb |
Optional, either missing 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 |
|
run.name |
Name of the analysis. The results will be
stored in a folder with this name in the current working directory
(use |
Based on the chromosome and probe position an absolute position is calculated according to
chromosome number * 1e9 + probe position. Chromosome column is converted to factor
and releveled according to
the levels of the chrom.table, so the only levels allowed are c(1:22, "X", "Y")
.
Currently only human genome support without mitochondrial DNA.
No values are returned. Instead, the datasets and annotation columns are stored in
separate files in the data
folder in the directory specified in run.name
.
If assemble.data
has run succesfully, the integrated.analysis function can be performed.
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl
#load the datasets and the samples to run the integrated analysis data(expr.data) data(acgh.data) data(samples) #assemble the data assemble.data(dep.data = acgh.data, indep.data = expr.data, dep.id="ID", dep.chr = "CHROMOSOME", dep.pos = "STARTPOS", dep.ann = colnames(acgh.data)[1:4], dep.symb="Symbol", indep.id="ID", indep.chr = "CHROMOSOME", indep.pos = "STARTPOS", indep.ann = colnames(expr.data)[1:4], indep.symb="Symbol", overwrite = TRUE, run.name = "chr8q")