# A package to produce metagene plots

## Documentation for package ‘metagene’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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.