A package to produce metagene plots


[Up] [Top]

Documentation for package ‘metagene’ version 1.0.0

Help Pages

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.