RDocumentation
Moon
Learn R
Search all packages and functions
⚠️
There's a newer version (1.32.0) of this package.
Take me there.
SLGI (version 1.30.0)
Synthetic Lethal Genetic Interaction
Description
A variety of data files and functions for the analysis of genetic interactions
Copy Link
Copy
Link to current version
Version
Version
1.32.0
1.30.0
1.28.0
1.26.0
Down Chevron
Version
1.30.0
License
Artistic-2.0
Maintainer
Nolwenn Le Meur
Last Published
January 1st, 1970
Functions in SLGI (1.30.0)
Search functions
AtongPair
Data frame the pair of yeast gene tested in Tong et al. 2004.
byComplex
Evaluate protein co-membership within cellular organizational units
AtongFnDomain
The functional domains shared by the tested pairs in Tong et al experiment.
compare
Compare observed data to expected in permutation models
comemberIn
Retrieve the biological complexes.
Atong
Systematic genetic analysis with ordered arrays of yeast deletion Tong et. al. (2004).
domainDist
Finds the number of gene sets for each shared domain
Boeke
Incidence matrix of Synthetic Lethal interaction from the Boeke Lab
congruence
Calculate congruence score between pairs of of genes sharing pattern of synthetic genetic interactions (Ye et al. (2005)).
createSquareMatrix
Create a square matrix
getInteraction
Count genetic interactions within and between cellular organizational units
getSharedInteraction
Calculate the number of shared synthetic genetic interactions between pairs of genes.
getSharedDomains
Find domains shared by a given list of gene names.
dSLAM.GPL1444
dSLAM platform used for Synthetic Lethal screens in the Boeke Lab
getTestedPairs
Find interacting and non-interacting tested pairs from an genetic interaction matrix.
essglist
The list of yeast essential genes
getUniquePairs
Find unique pairs from an genetic interaction matrix.
gi2005
Genetic Interaction Data (EMAP) from the yeast early secretory pathway
gi2007
Synthetic Genetic Interaction data from Collins et al
gi2Interactome
Reduce genetic interactions matrix
twoWayTable
Generate two-way table for genetic interaction data
topInteraction
Extract interacting biological complexes
SGD.SL
Interaction data from the Saccharomyces Genome Database
sharedBy
Find the gene pairs that share a domain.
TFmat
Transcription Factor Binding Affinities
test2Interact
Summarize genetic interactions within or between cellular organizational units
SGA
Systematic genetic analysis with ordered arrays of yeast deletion.
seqMatcherAlign
Functions to do local alignment of two sequences using EMBOSS matcher
withinComplex
Search for protein co-membership within complexes.
modelSLGI
Permutation model for assessing synthetic genetic interactions in cellular organizational units.
normInteraction
Normalize a matrix of biological interactions
hyperG
Hypergeometric test
iSummary
Summarize cellular organizational units sharing genetic interaction
SDL
The Association matrix for the synthetic dosage lethal screens in Yeast.
sharedInt
List shared genetic interactions between genes
plot
Graphical method to represent the result of the modelSLGI .
siResult-class
A class for representing the result of the SLGI graph permutation model.