| annoXeset | Function for cross annotating a mouse expression set with... |
| annoXMouseHuman | Function for annotating and cross annotating top table of... |
| auxBiplot | Plots a boxplot of qVar over different categories of BiVar.... |
| calcFCH | A function that given a matriz of log2FCH calculates the... |
| CalculateCorrMatrix | Internal function of DoCorrelationPlotwithStarts. |
| colChoice.2 | Defining colors from a pattern |
| collapseduplicatesids | A function that collapse annotation of probes that mapp to... |
| collapsefcn | Given a vector of characters a b c it returns a single... |
| ComBat_MSF | Function that runs the original Combat script but returns... |
| cor.prob.pearson | calculates the p-values for the pair-wise pearson correlation... |
| cor.prob.spearman | calculates the p-values for the pair-wise spearman... |
| CorrelationHeatmap_Samples | Function that given a data base of continuos variables,... |
| Create_GSEAInput | A function that creates ranked files for GSEA |
| CreateOutputsMA | A function that creates a table with the results of limma... |
| deletePathway | A function that deletes pathways whose frequency is greater... |
| dis.cors | Internal function of DoCorrelationPlotwithStarts. |
| doBarPlot | A function that creates a barplot with a table for contrasts |
| DoCluster | Save output of a heatmap built from a decision matrix and... |
| DoCluster2 | Save output of a heatmap built from a decision matrix and... |
| doClusterTableFCH_fromMatrix | A function that creates a heatmap with column indicators on... |
| DoCorrelationPlotwithStarts | Function that given a correlation matrix and the pvalues,... |
| DoHeatmap | A function that draws a heatmap based on a matrix |
| DoHeatmap.3_MSF | A function that draws a heatmap based on a matrix |
| DoHeatmapSamples | A function that draws a heatmap based on a matrix |
| doSwindellPlot | A function that produce Swindell plots showing the... |
| doVenn | A function to draw Venn Diagrams from Decision Matrices |
| dowordcloud | Creates a wordcloud representin Fold changes and color coded... |
| ellipsoid.Fox | Function from John Fox that is called by scatter3d.Fox. |
| firstelementfcn | It returns the first element non-NA from a vector. |
| from1list2D | A function that converts a list of genelist into a Decision... |
| from2list2D | A function that converts a two class lists of up and down... |
| FromEbfit2DEGTable | creates an output table including genes that are declared... |
| FromEbfit2Table | creates an output table including all genes in ebfit |
| fromPtoCol | Internal function of dowordcloud. |
| getAllDEGs | Given a Decision matrix (output of decideTests), it returns... |
| getAnnotationTable | A function that creates an Annotation table for microorrays... |
| getgray | A function that assigns levels of gray to a vector |
| getMeanCI.by.Path | Function given a value in y and a collection of pathways |
| getModels_Caret | A function that tells you what are most N disimilar models... |
| getMultipleMeanCI.by.Path | Function given a collection of pathways, returns the summary... |
| getMultipleZscore.by.Path | Function given a collection of pathways, returns the Z score... |
| getPCAs | Extraction of principal components |
| getstar | A function that returns an object of type character equal to... |
| getSymbolByX | A function that |
| getZs | A function that calculates Z-scores and p-values |
| getZscore.by.Path | Function given a T statistic and a collection of pathways,... |
| ggDendrogram_MSF | Function that prints a dendogram using ggplot. Was modified... |
| givecolnames | A function that changes the column names of a matrix by... |
| heatmap.3 | A function that creates a dataframe to be used as input to... |
| makeGSEApheno | A function that creates genotypes for GSEA |
| makenames_MSF | A function that given common gene names in dermatology,... |
| mgsub | A function that replace values in a vector |
| multiplot | Multiple plot function |
| mylog10 | A function that returns the base 10 logarithm of the... |
| mylog2 | A function that returns the base 2 logarithm of the... |
| nmissing | Returns the number of missing values in a vector |
| normDataWithin | Summarizes data. Norms the data within specified groups in a... |
| prepareGSEArnk | A function that prepares GSEA ranked data |
| prettyp | A function that express a number using scientific notation or... |
| processGMT | Function for parsing a GMT gene set list |
| readGmt | A function that reads GMT files |
| readGmt2 | Function for reading a GMT file of gene set collection |
| renamecols | A function that changes the names of a dataframe columns |
| Resume | A function that prepare the results of a linear model fit |
| RunCombat | Function that runs the original Combat script where no model... |
| RunCombatMat | Function that runs the original Combat script where no model... |
| RunCombat_MSF | Function that runs the original Combat script where no model... |
| RunGeneSetCollection_MSF | A function that runs analyzeGeneSetCollections function |
| Run.swindel.sims | A function that produce Swindell plots showing the... |
| scatter3d.Fox | Function that draws an scatterplot with three dimensions with... |
| sciNotation | A function that returns a scientific notation of a p value |
| stackchar | A function that concatenates a vector of character using... |
| summarySE | Summarizes data. |
| summarySEwithin | ## Summarizes data, handling within-subjects variables by... |
| swindel.sims | A function that runs simulations to produce Swindell plots to... |
| uniquenona | A function that given a vector returns only the unique... |
