Replication Timing Profiling using DNA Copy Number


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Documentation for package ‘Repliscope’ version 1.0.0

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compareRatios A function to compare two replication profiles
Dbf4myc Sequence read coverage ratios for S.cerevisiae Dbf4-9myc sample.
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.
MFA Replication profile for wild type DS2 H.volcanii
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. Normalisation factor used is stored in 'ratioFactor' column and also passed as the dataframe comment. To extract it, use 'attributes(mergedBed)$comment'
normalizeRatio A function to normalise ratio values from 'ratio' column of the provided dataframe to fit biologically-relevant scale. It scales values either using supplied 'rFactor' value or automatically to best fit 1 to 2 scale. Normalisation factor used is stored in 'ratioFactor' column and also passed as the dataframe comment. To extract it, use 'attributes(mergedBed)$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.
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.
W303 Sequence read coverage ratios for wild type S.cerevisiae W303
W303norm Sequence read coverage ratios for wild type sample
W303_G2 Sequence read coverage for wild type S.cerevisiae W303 non-replicating sample.
W303_S Sequence read coverage for wild type replicating sample