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SLGI (version 1.28.0)

Synthetic Lethal Genetic Interaction

Description

A variety of data files and functions for the analysis of genetic interactions

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Version

Version

1.28.0

License

Artistic-2.0

Maintainer

Nolwenn Le Meur

Last Published

February 15th, 2017

Functions in SLGI (1.28.0)

createSquareMatrix

Create a square matrix
comemberIn

Retrieve the biological complexes.
compare

Compare observed data to expected in permutation models
AtongFnDomain

The functional domains shared by the tested pairs in Tong et al experiment.
AtongPair

Data frame the pair of yeast gene tested in Tong et al. 2004.
Boeke

Incidence matrix of Synthetic Lethal interaction from the Boeke Lab
byComplex

Evaluate protein co-membership within cellular organizational units
congruence

Calculate congruence score between pairs of of genes sharing pattern of synthetic genetic interactions (Ye et al. (2005)).
domainDist

Finds the number of gene sets for each shared domain
Atong

Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004).
getInteraction

Count genetic interactions within and between cellular organizational units
essglist

The list of yeast essential genes
getUniquePairs

Find unique pairs from an genetic interaction matrix.
dSLAM.GPL1444

dSLAM platform used for Synthetic Lethal screens in the Boeke Lab
gi2005

Genetic Interaction Data (EMAP) from the yeast early secretory pathway
getSharedDomains

Find domains shared by a given list of gene names.
gi2007

Synthetic Genetic Interaction data from Collins et al
getSharedInteraction

Calculate the number of shared synthetic genetic interactions between pairs of genes.
getTestedPairs

Find interacting and non-interacting tested pairs from an genetic interaction matrix.
gi2Interactome

Reduce genetic interactions matrix
test2Interact

Summarize genetic interactions within or between cellular organizational units
seqMatcherAlign

Functions to do local alignment of two sequences using EMBOSS matcher
TFmat

Transcription Factor Binding Affinities
SGA

Systematic genetic analysis with ordered arrays of yeast deletion.
normInteraction

Normalize a matrix of biological interactions
modelSLGI

Permutation model for assessing synthetic genetic interactions in cellular organizational units.
twoWayTable

Generate two-way table for genetic interaction data
topInteraction

Extract interacting biological complexes
plot

Graphical method to represent the result of the modelSLGI .
SDL

The Association matrix for the synthetic dosage lethal screens in Yeast.
withinComplex

Search for protein co-membership within complexes.
sharedInt

List shared genetic interactions between genes
hyperG

Hypergeometric test
siResult-class

A class for representing the result of the SLGI graph permutation model.
iSummary

Summarize cellular organizational units sharing genetic interaction
SGD.SL

Interaction data from the Saccharomyces Genome Database
sharedBy

Find the gene pairs that share a domain.