integrated.analysis {SIM} | R Documentation |
Runs the Integrated Analysis to test for associations between DNA copy number measurements and gene expression measurements on the same set of samples.
integrated.analysis(samples, input.regions="all chrs", adjust=FALSE, zscores=FALSE, method=c("auto", "asymptotic", "permutations", "gamma"), run.name=NULL)
samples |
vector with either the names of the columns in the dependent and independent data corresponding to the samples, or a numerical vector containing the column numbers to include in the analysis, e.g. 5:10 means columns 5 till 10. Make sure that both datasets have the same number of samples with the same column names! |
input.regions |
vector indicating the regions to be analyzed. Can be defined in four ways:
1) predefined input region: insert a predefined input region, choices are: "all chrs" , "all chrs auto" , "all arms" , "all arms auto" In the predefined regions "all arms" and "all arms auto" the arms 13p, 14p, 15p, 21p and 22p are left out, because in most studies there are no or few probes in these regions. To include them, just make your own vector of arms. 2) whole chromosome(s): insert a single chromosome or a list of chromosomes as a vector: c(1, 2, 3) . 3) chromosome arms: insert a single chromosome arm or a list of chromosome arms like c("1q", "2p", "2q") .4) subregions of a chromosome: insert a chromosome number followed by the start and end position like c("chr1\_1-1000000") These regions can also be combined, e.g. c("chr1_1-1000000","2q", 3) . See details for more information. |
adjust |
Confounders for which the integration-test must be adjusted, such as tumor type, location, gender, etc. Either a formula with a factor of a vector with names with the same length as samples or FALSE. A formula with a vector can e.g. be: Y~factor(subtype) where subtype is a vector with the same length as samples with names like: subtype = c("tumor","tumor", "normal","normal", etc...) See ?globaltest for more information. |
zscores |
Boolean , indicates whether the z-scores are calculated (takes longer time to run). If z-scores=FALSE, only p-values are calculated. |
method |
The method for calculation of the p-values. Use method = "asymptotic" for the full asymptotic distribution of the test statistic, method = "gamma" for the gamma (= scaled chi-squared) approximation to that distribution and method = "permutations" for a permutation p-value. The recommended default: method = "auto" chooses the permutations method if the number of possible permutations does not exceed 10,000 and the asymptotic otherwise. See ?globaltest for more information. |
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. |
The Integrated Analysis is a regression of the independent data
on the dependent features. In most cases, the dependent data will be the copy
number measurements from array-CGH and the independent data the expression array
values. The regression itself is done using the globaltest
, which means
that the genes in a region (e.g. a chromosome arm) are tested as a gene set. The
individual associations between each copy number probe and each expression probe
are calculated as z-scores (standardized influences, see ?globaltest
).
This function splits the datasets into separate sets for each region (as
specified by the input.regions
) and runs the analysis for each region
separately.
When running the Integrated Analysis for a predefined input region, like "all arms"
and "all chrs"
, output can be obtained for all input regions, as well as
subsets of it. But note that the genomic unit must be the same: if integrated.analysis
was run using chromosomes as units, any of the functions and plots must also use chromosomes
as units, and not chromosome arms. Similarly, if integrated analysis
was run using
chromosome arms as units, these units must also be used to produce plots and outputs.
For example if the input.regions = "all arms"
was used, p-value plots
(see sim.plot.pvals.on.region can be produced by inserting the input.regions = "all arms"
,
but also for instance "1p"
or "20q"
. However, to produce a plot of the whole
chromosome, for example chromosome 1, the integrated should be re-run with input.region=1
.
The same goes for "all chrs": p-value plots etc. can be produced for chromosome 1,2 and so on...
but to produce plots for an arm, the integrated.analysis
should be re-run for that region.
This also goes for subregions of the chromosome like "chr1_1-1000000".
No values are returned. Instead, the results of the analysis are stored
in the subdirectories of the directory specified in run.name
. E.g. the z-score matrices
are saved in subfolder intermediate.data. The following functions can be used to
visualize the data:
1) |
sim.plot.zscore.heatmap (pdf, only possible when zscores=TRUE ) |
2) |
sim.plot.pvals.on.region (pdf) |
3) |
sim.plot.pvals.on.genome (pdf) |
|
Other functions can be used to tabulate the results: |
1) |
tabulate.pvals (data.frame) |
2) |
tabulate.top.dep.features (txt) |
3) |
tabulate.top.indep.features (txt, only possible when zscores=TRUE |
Marten Boetzer, Melle Sieswerda, Renee X. de Menezes R.X.Menezes@lumc.nl
SIM
, assemble.data
, 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
,globaltest
#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, 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") #run the integrated analysis integrated.analysis(samples=samples, input.regions=c(8), adjust=FALSE, zscores=TRUE, method="auto", run.name ="chr8")