Dbf4myc                 Sequence read coverage ratios for S.cerevisiae
                        Dbf4-9myc sample.
MFAseq                  Replication profile for wild type DS2
                        H.volcanii
TrepDF                  Trep data calculated from syncSeq[["data"]]
W303                    Sequence read coverage ratios for wild type
                        S.cerevisiae W303
W303_G2                 Sequence read coverage for wild type
                        S.cerevisiae W303 non-replicating sample.
W303_S                  Sequence read coverage for wild type
                        S.cerevisiae W303 replicating sample
W303norm                Normalised sequence read coverage ratios for
                        wild type S.cerevisiae W303
calcTrep                A function to calculate Trep values from a
                        sync-seq experiment calcTrep function fits a
                        Boltzman sigmoid function into relative copy
                        number datapoints for every genomic bin of the
                        provided sync-seq merged dataframe. It then
                        extracts time at which half of the cells have
                        this genomic bin replicated (Trep). The output
                        of the function is a dataframe containing Trep
                        and TrepErr data for every genomic bin in a
                        BED-like format.
compareRatios           A function to compare two replication profiles
guide                   Guide dataframe for plotting smoothed sortSeq
                        data
loadBed                 Load a BED formatted file.
makeGenome              A helper function to create a gemome dataframe
makeLabels              A helper function to create axis ticks and
                        human readable labels.
makeRatio               A function to calculate 'score' ratio between
                        two bed dataframes makeRatio merges two
                        supplied bed dataframes, calculates ratio of
                        their "score" values normalises the ratio by
                        the 'score' sums.
normaliseRatio          A function to normalise ratio values from
                        'ratio' column of the provided dataframe to fit
                        biologically-relevant scale. It scales values
                        either using supplied 'rFactor' value or
                        automatically to best fit 1 to 2 scale (the
                        upper limit of the scale may be adjusted with
                        the upperLimit parameter). Normalisation factor
                        used is stored in 'ratioFactor' column and also
                        passed as the dataframe comment. To extract it,
                        use 'attributes(mergedBed)$comment'
plotBed                 A function to boxplot 'score' column of a BED
                        dataframe, per unique chromosome name in the
                        'chrom' column. The resulting plot also
                        highlights outliers based on the inter quartile
                        range (IQR). The genome wide median is plotted
                        as a pink line through the boxplots.
plotCoverage            A function to scatterplot 'score' column of a
                        BED dataframe plotCoverage function plots
                        values in the 'score' column of the supplied
                        bed dataframe as a function of chromosome
                        coordinates. The genome wide median is plotted
                        as a pink line.
plotGenome              plotGenome: plot replication profile.
plotRatio               A function to plot a histogram of supplied
                        ratio vector plotRatio plots histogram of
                        values in a supplied vector using ggplot2 and
                        highlights interval between 1 and 2 in green.
plotTrep                A function to scatterplot 'Trep' column of a
                        Trep dataframe plotTrep function plots values
                        in the 'Trep' column of the supplied dataframe
                        as a function of chromosome coordinates. The
                        genome wide median is plotted as a pink line.
rmChr                   A function to remove single chromosome data
                        from a bed dataframe
rmOutliers              A function to remove outliers from the "score"
                        column of a supplied bed dataframe There are
                        three methods: max, IQR and median. Max is used
                        to remove 1 or more maximum values; IQR uses
                        interquartile range to detect outliers, while
                        median method can be used to remove data based
                        on genome-wide median.
runGUI                  A function to launch Repliscope in interactive
                        mode (Shiny app).
sacCer3                 S.cerevisiae genome information
smoothRatio             A function to smooth ratio values using cubic
                        smoothing spline smoothRatio function splits
                        values from 'ratio' column by chromosome and
                        based the supplied 'groupMin' and 'split'
                        parameters and then applies smooth.spline()
                        function from R stats package. The supplied
                        dataframe may contain multiple ratios, i.e.
                        ratios produced using multiple replicating
                        samples and/or multiple non-replicating
                        samples. This must be reflected in 'name.rep'
                        and 'name.nonRep' columns. In other words,
                        different ratio dataframes may be merged using
                        rbind() function before calling smoothRatio()
                        function.
sortSeq                 Replication profiles for wild type and
                        Dbf4-9myc S.cerevisiae samples
syncSeq                 Replication profiles budding yeast
                        arrest-release samples
trimRatio               A function to remove outliers from the "ratio"
                        column of a supplied ratio dataframe trimRatio
                        is applied to the calculated ratio of read
                        counts from a replicating to a non-replicating
                        samples.
