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SVDAnalyzer

Performs Singular Value Decomposition to gene sets to test whether a set of genes is significantly differentially expressed.

In the SVD method the expression values of multiple variables (=genes) are captured into one variable called metagene. This metagene is the main component of the SVD and captures most of the variation in the expression matrix.

The main idea of SVDAnalyzer is to summarize the expression values of a sample in a gene set into a single value called activity level. The activity level is defined for each sample in each pathway by using SVD. The activity level can be regarded as a weighted sum of the expression values, where the weights are given by the first metagene.

The activity levels are, then, used to make comparisons between the sample groups. These comparisons can be made by calculating e.g. t statistic for each pathway.

Required packages

Install package 'genefilter' from R: source('http://bioconductor.org/biocLite.R'); biocLite(); Install package 'csbl.go' from CSBL pages: csbl.go (requires package RUnit) Install package 'Category' from R: biocLite('Category');

Version 1.0
Bundle microarray
Categories Analysis Pathway
Authors Minna Miettinen (Minna.Miettinen@Helsinki.FI)
Issue tracker View/Report issues
Requires R ; libxml2-dev (DEB) ; MASS (R-package) ; KEGG.db (R-bioconductor) ; genefilter (R-bioconductor) ; csbl.go (R-package) ; Category (R-bioconductor)
Source files component.xml analyzer.R
Usage Example with default values

Inputs

Name Type Mandatory Description
annotation CSV Mandatory Gene annotation table. Parameters sourceId and targetId specify the columns containing the names of the genes and respective annotations.
expr LogMatrix Mandatory The expression values of the genes. First column should contain the same gene identifiers as the sourceId column in the annotation table. The number of rows i.e. genes, can be more than the number of sourceIds in the annotation table. However, expression values for all the sourceIds should be found in the expr table.
sampleGroupTable SampleGroupTable Mandatory SampleGroupTable represents the relation between a sample and its group. Table should contain at least two groups. The activity levels are determined by performing SVD using expression data from all samples. However, only two groups can be selected to make comparisons with t-test. These groups are selected with parameters Group1, and Group2.

Outputs

Name Type Description
report Latex Latex report of the SVD results: activity level plots of interesting gene sets and a table presenting statistics for each gene set.
resultTable CSV Table presents analysis results in ascending order according to permuted p-value.

Parameters

Name Type Default Description
database string "GO" The gene set identifiers used. The possible choices are "GO", "KEGG" or "other".
group1 string "" The group whose expressions will be compared against Group2.
group2 string "" The group whose expressions will be compared against Group1.
nPath int 50 The number of top pathways presented in the latex report.
nperm int 10000 The number of permutations produced while evaluating p value for a pathway.
pPlots float 0.01 The pathways to be plotted. The activity levels of pathways with the p values smaller than Pplots are plotted. An error might occur if too high value is chosen for Pplots.
pagebreak boolean false Tells if the resulting document should start with a page break.
section string "" Section title for the table container or an empty string in case no section is selected to be generated.
sectionType string "subsection" Type of LaTeX section: usually one of: section, subsection, or subsubsection. No section statement is written if section title is empty.
seed int 12345 Seed number for the pseudo random number generator
sourceId string "GeneId" Character string specifying the column of gene identifiers in the input annotation.
targetId string "GeneSetId" Character string specifying the column of gene set identifiers in the input annotation.
threshold int 10 The minimum number of genes in a gene set.

Test cases

Test case Parameters IN
annotation
IN
expr
IN
sampleGroupTable
OUT
report
OUT
resultTable
case1 properties annotation expr sampleGroupTable report resultTable

group1 = low,
group2 = high

case2 properties annotation expr sampleGroupTable report resultTable

pPlots = 0.01,
group1 = trans,
group2 = normal,

case3 properties annotation expr sampleGroupTable report resultTable

pPlots = 0.01 ,
database = KEGG,
group1 = N,
group2 = C,
threshold = 1,
seed = 35726,
nPath = 20

case4 properties annotation expr sampleGroupTable report resultTable

database = KEGG,
nperm = 500,
sourceId = Uniprot,
targetId = Pathways,
threshold = 3,
group1 = low,
group2 = high


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