applyOnGroups | Apply a function on every groups of the main data structure |
binBootstrap | Estimate mean and confidence interval of a column using bootstrap. |
binMatrix | Bin matrix columns |
bootstrapAnalysis | Perform the bootstrap analysis |
getDataFrame | Convert the bootstrapped data into a data.frame |
getGenes | Fetch the annotation of all genes. |
getGenesBiomart | Fetch the annotation of all genes from biomart. |
mergeMatrix | Convert list of vectors in matrix for a single group |
parseBamFile | Parse a single bam file |
parseBamFiles | Parse multiple bamFiles |
parseFeatures | Parse an experiment using a list of features |
parseRegions | Parse an experiment using regions that can be of different length. |
plotGraphic | Produce a plot with based on a data.frame |
plotMatrices | Create a graph |
prepareBamFiles | Prepare bam files before parsing. |
prepareFeatures | Convert a list of IDs into a GRangesList |
prepareGroups | Distribute the bam filenames in their respective groups. |
prepareRegions | Parse bed files and convert them in a list of GRangesList. |
rawCountsToRPM | Convert the raw counts into reads per million aligned (rpm) |
removeControls | Substract controls from a single group |
scaleVector | Scale the values of a vector to fit with predetermined size |
scaleVectors | Resize the vectors of every group so they have the same length. |