DoISVA.v2: Feature selection using independent surrogate variables...
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments Value Author(s) References Examples

Given a data matrix and a phenotype of interest, this function performs feature selection to identify features associated with the phenotype of interest in the presence of potential confounding factors. The algorithm first finds the variation in the data matrix not associated with the phenotype of interest (using a linear model), and subsequently performs Independent Component Analysis (ICA) on this residual variation matrix. The number of independent components to be inferred can be prespecified or estimated using Random Matrix Theory. Independent Surrogate Variables (ISVs) are constructed from the independent components and provide estimates of the effect of confounders on the data. If potential confounders are unknown (default NULL option) there will be as many ISVs as there are independent components in the residual variation space. If potential confounders are known (either exactly or subject to error/uncertainty) the algorithm will select only those independent components that correlate with the confounders. If potential confounders are specified it can happen that ISVA will not select any ISVs because none of the independent components correlates with the confounders. In this scenario ISVA should be rerun with the default (NULL) option. The constructed ISVs are finally included as covariates in a multivariate regression model to identify features that correlate with the phenotype of interest independently of the potential confounders.

1 2	DoISVA.v2(data.m, pheno.v, cf.m = NULL, factor.log, pvthCF = 0.01, th = 0.05, ncomp = NULL)

`data.m`	Data matrix: rows label features, columns label samples. It is assumed that number of features is much larger than number of samples.
`pheno.v`	Numeric vector of length equal to number of columns of data matrix. At present only numeric (ordinal) phenotypes are supported, so categorical phenotypes are excluded.
`cf.m`	Matrix of potential confounding factors. Rows label samples, Columns label confounding factors, which may be numeric or categorical. The default option (NULL) is for the case where potential confounding factors are not known or irrelevant.
`factor.log`	A logical vector of same length as columns of `cf.m`. FALSE indicates factor is to be treated as a numeric, TRUE as categorical.
`pvthCF`	P-value threshold to call a significant association between an independent surrogate variable and a confounding factor. By default this is 0.01.
`th`	False discovery rate threshold for feature selection. By default this is 0.05.
`ncomp`	Number of independent surrogate variables to look for. By default this is NULL, and estimation is performed using Random Matrix Theory.

A list with following entries:

`spv`	Sorted P-values.
`rk`	Ranked index of features.
`qv`	Estimated sorted q-values (False Discovery Rate).
`ndeg`	Number of differentially altered features.
`deg`	Indices of differentially altered features.
`lm`	Matrix of significant feature regression statistics and P-values.
`isv`	Matrix of selected independent surrogate variables (ISVs).
`nsv`	Number of selected ISVs.
`pvCF`	P-value matrix of associations between factors (phenotype of interest plus confounding factors) and inferred ISVs. Note that this may be a larger set than the selected ISVs.
`selisv`	Column indices of selected ISVs.

Andrew E Teschendorff

Independent Surrogate Variable Analysis to deconvolve confounding factors in large-scale microarray profiling studies. Teschendorff AE, Zhuang JJ, Widschwendter M. Bioinformatics. 2011 Jun 1;27(11):1496-505.

### Example

## load required libraries
library(isva)

### load in simulated data
data(simdataISVA);
data.m <- simdataISVA$data;
pheno.v <- simdataISVA$pheno;

## factors matrix (two potential confounding factors, e.g chip and cohort)
factors.m <- cbind(simdataISVA$factors[[1]],simdataISVA$factors[[2]]);
colnames(factors.m) <- c("CF1","CF2");

### Estimate number of significant components of variation
rmt.o <- EstDimRMT(data.m);
print(paste("Number of significant components=",rmt.o$dim,sep=""));
### this makes sense since 1 component is associated with the
### the phenotype of interest, while the other two are associated
### with the confounders
ncp <- rmt.o$dim-1 ;

### Do ISVA
### run with the confounders as given
isva.o <- DoISVA(data.m,pheno.v,factors.m,factor.log=rep(FALSE,2),pvthCF=0.01,
th=0.05,ncomp=ncp);

### Evaluation (ISVs should correlate with confounders)
### modeling of CFs
print(cor(isva.o$isv,factors.m));
### this shows that CFs are reconstructed fairly well

### sensitivity (fraction of detected true positives)
print(length(intersect(isva.o$deg,simdataISVA$deg))/length(simdataISVA$deg));

### PPV (1-false discovery rate)
print(length(intersect(isva.o$deg,simdataISVA$deg))/length(isva.o$deg));

### run not knowing what confounders there are and with ncp=3 say.
isva2.o <- DoISVA(data.m,pheno.v,cf.m=NULL,factor.log=rep(FALSE,2),pvthCF=0.01,
th=0.05,ncomp=3);

### sensitivity (fraction of detected true positives)
print(length(intersect(isva2.o$deg,simdataISVA$deg))/length(simdataISVA$deg));

### PPV (1-false discovery rate)
print(length(intersect(isva2.o$deg,simdataISVA$deg))/length(isva2.o$deg));