assemble.data {SIM} | R Documentation |
Assembles the copy number and expression data and annotation.
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)
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. |
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.
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl
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
#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")