as.list-method |
Class "MetaArray" ~~~ |
clinical |
Functions to retrieve and assign |
clinical.sum |
Function to calculate summaries of clinical data |
clinical<- |
Functions to retrieve and assign |
clinical<--method |
Functions to retrieve and assign |
clinical<--method |
Replacement Methods for 'MetaArray' object |
clinical<--methods |
Replacement Methods for 'MetaArray' object |
colIntersect |
Function to find intersect in columns of a data.frame |
ColonData |
Example dataset for meta-analysis of microarray |
commonGenes |
Function to compute number of common genes in ordered gene lists |
compute.RQ |
Function to compute R and Q statistics as defined in - see References |
computeAlpha |
Function to do compute tunning parameter alpha |
computeOrdering |
Function to compute ordered gene lists |
conting.tab |
Contingency table from gene lists |
cv.filter |
Microarray probes filtering |
datanames |
Functions to retrieve and assign |
datanames<- |
Functions to retrieve and assign |
datanames<--method |
Functions to retrieve and assign |
datanames<--method |
Replacement Methods for 'MetaArray' object |
datanames<--methods |
Replacement Methods for 'MetaArray' object |
entitybuild2 |
Function to calculate test statistic for microarray data |
ES.GeneMeta |
Wrapper function for combining the effect size as implemented in GeneMeta package |
ES.GeneMeta.res |
Wrapper function for combining the effect size as implemented in GeneMeta package |
flip |
Function to flip data frames |
fold.change |
Function to do compute fold change between two groups |
GEDM |
Functions to retrieve and assign |
GEDM<- |
Functions to retrieve and assign |
GEDM<--method |
Functions to retrieve and assign |
GEDM<--method |
Replacement Methods for 'MetaArray' object |
GEDM<--methods |
Replacement Methods for 'MetaArray' object |
gene.list |
Intersect of gene lists |
gene.select.FC |
Function to select genes according to fold change |
join.DEG |
Function to join vectors of differentially expressed genes to one list |
join.results |
Function to join results from meta-analysis to one list |
make.matrix |
Function to make matrix for heatmap to compare results of several methods |
MAP.genes |
Function to do assign probesets IDs to patterns |
MAP.Matches |
Wrapper function for MAP-Matches method |
MAP.Matches.res |
Wrapper function for MAP-Matches method |
MAPmatrix |
Function to summarize binary matrix |
MAPsig1 |
Pattern signifficance |
MAPsig2 |
Pattern signifficance |
MCtest |
Monte Carlo permutation test |
mergedata |
Function to merge data from MetaArray object |
mergeExprs2 |
Function to merge ExpressionSet object |
meta.test |
Function to compute T-statistic and p-value in meta-analysis |
MetaArray-class |
Class "MetaArray" ~~~ |
metagene |
Function to do extract row from list of data.frames |
metaheat |
Display Data as Heatmap |
metaheat2 |
Function to plot heatmap |
metalist.to.matrix |
Function to do convert list to matrix |
metaMA |
Wrapper function for effect size or p-value combination methods |
metaMA.res |
Wrapper function for effect size or p-value combination methods |
METRADISC |
Wrapper function for METRADISC method |
METRADISC.res |
Wrapper function for METRADISC method |
multExpFDR |
Function for Meta-analysis of gene expression data |
patternMatch |
Function to count soft pattern matches |
patternMatch.strong |
Function to count strong pattern matches |
patternmatrix |
Function to split binary vectors to matrix. |
patternToString |
Function to convert rows of a matrix to strings |
performSOGL |
Function to perform analysis using Similarity of Ordered Gene Lists |
plot-method |
Class "MetaArray" ~~~ |
plot.SOGLresult |
Function to plot an object of class SOGLresult |
plotES |
Function to do plots in combination of effect size method |
plotgene |
Function to visuaze change in expression of one gene |
plotgene2 |
Function to visuaze change in expression of one gene |
plotpattern |
Function to do plot signifficance of Meta-Analysis Patterns |
plotQvsChi |
Function to plot quantiles of Cochran's Q statistic and Chi-square quantiles. |
posterior.mean |
Function to calculate posterior mean differential expression |
prelimScore |
Function compute preliminary Similarity Score for Ordered Gene Lists |
prepareData |
Function to prepare data |
preparePermutations |
Function to prepare permutation and subsamples |
print-method |
Class "MetaArray" ~~~ |
probs.to.matrix |
Function to convert list to matrix |
RandomScore |
Function to do compute random and subsampled similarity score |
rank.genes |
Rank genes |
rank.genes.adv |
Function to rank genes |
RankProduct |
Wrapper function for RankProduct method |
RankProduct.res |
Wrapper function for RankProduct method |
ratio |
Function to calculate the ratio of co-significant: expected/observed |
sd.filter |
Microarray probes filtering |
selectAlpha |
Function to select the most optimal alpha parameter |
selectClass |
Function to select class labels from MetaArray object |
selectGenes |
Function to select genes that account for Similarity score |
show-method |
Class "MetaArray" ~~~ |
sigScore |
Function to calculate signifficance of similarity score |
T.select |
Function to help with selection of threshold for T-statistics |
test.group.shuffle |
Function to do compute test statistic iterativelly |
VennMapper |
Wrapper function for VennMapping |
VennMapper.res |
Wrapper function for VennMapping |
Z |
Function to compute Z-statistics in contingency table |
zScoreFDR |
Function for Meta-analysis of gene expression data |
zScorePermuted |
Function for Meta-analysis of gene expression data |
zScores |
Function for Meta-analysis of gene expression data |