# Synthetic Lethal Genetic Interaction

## Documentation for package ‘SLGI’ version 1.4.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

Atong | Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004).
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.
Boeke2006 | Incidence matrix of Synthetic Lethal interaction from the Boeke Lab
Boeke2006raw | Incidence matrix of Synthetic Lethal interaction from the Boeke Lab
byComplex | Evaluate protein co-membership within cellular organizational units
comemberIn | Retrieve the biological complexes.
compare | Compare observed data to expected in permutation models
compare,siResult-method | Compare observed data to expected in permutation models
congruence | Calculate congruence score between pairs of of genes sharing pattern of synthetic genetic interactions (Ye et al. (2005)).
createSquareMatrix | Create a square matrix
domainDist | Finds the number of gene sets for each shared domain
dSLAM | dSLAM platform used for Synthetic Lethal screens in the Boeke Lab
dSLAM.GPL1444 | dSLAM platform used for Synthetic Lethal screens in the Boeke Lab
essglist | The list of yeast essential genes
getAlignStats | Functions to do local alignment of two sequences using EMBOSS matcher
getFASTAname | Obtain sequence name from FASTA object
getInteraction | Count genetic interactions within and between cellular organizational units
getSharedDomains | Find domains shared by a given list of gene names.
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.
getUniquePairs | Find unique pairs from an genetic interaction matrix.
gi2005 | Genetic Interaction Data (EMAP) from the yeast early secretory pathway
gi2005.metadata | Genetic Interaction Data (EMAP) from the yeast early secretory pathway
gi2007 | Synthetic Genetic Interaction data from Collins et al
gi2007.metadata | Synthetic Genetic Interaction data from Collins et al
gi2Interactome | Reduce genetic interactions matrix
hyperG | Hypergeometric test
iSummary | Summarize cellular organizational units sharing genetic interaction
modelSLGI | Permutation model for assessing synthetic genetic interactions in cellular organizational units.
normInteraction | Normalize a matrix of biological interactions
plot | Graphical method to represent the result of the modelSLGI .
plot,siResult,missing-method | Graphical method to represent the result of the modelSLGI .
plot,siResult-method | Graphical method to represent the result of the modelSLGI .
SDL | The Association matrix for the synthetic dosage lethal screens in Yeast.
seqMatcherAlign | Functions to do local alignment of two sequences using EMBOSS matcher
SGA | Systematic genetic analysis with ordered arrays of yeast deletion.
SGAraw | Systematic genetic analysis with ordered arrays of yeast deletion.
SGD.SL | Interaction data from the Saccharomyces Genome Database
SGD.SynGrowthDefect | Interaction data from the Saccharomyces Genome Database
SGD.SynRescue | Interaction data from the Saccharomyces Genome Database
sharedBy | Find the gene pairs that share a domain.
sharedInt | List shared genetic interactions between genes
show,siResult-method | A class for representing the result of the SLGI graph permutation model.
siResult-class | A class for representing the result of the SLGI graph permutation model.
SLchr | The Association matrix for the synthetic dosage lethal screens in Yeast.
test2Interact | Summarize genetic interactions within or between cellular organizational units
TFmat | Transcription Factor Binding Affinities
tong2004raw | Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004).
topInteraction | Extract interacting biological complexes
twoWayTable | Generate two-way table for genetic interaction data
withinComplex | Search for protein co-membership within complexes.