This class is a container for information on a specific 4C-seq experiment. Stored information includes raw reads, fragment data, and the experiment's viewpoint location.
Basic4Cseq offers filter functions for invalid 4C-seq reads. This function removes 4C-seq reads from a provided Sequence Alignment/Map (SAM) file that show mismatches in the restriction enzyme sequence.
This function extracts fragment data from a Data4Cseq object's rawFragments slot for visualization with the functions visualizeViewpoint and drawHeatmap . Relevant fragments are located within the chosen visualization range; the viewpoint itself can be excluded or included.
Basic4Cseq can create virtual fragment libraries from any BSgenome package or DNAString object. Two restriction enzymes have to be specified to cut the DNA, the read length is needed to check the fragment ends of corresponding length for uniqueness. Filter options (minimum and maximum size) are provided on fragment level and on fragment end level.
This function is a small convenience function to plot the results of simulateDigestion as a histogram. Minimum and maximum fragment lengths can be specified to visualize a specified interval of the fragment data.
This method draws a fragment-based heatmap-like plot for 4C-seq data around a given viewpoint. For a given number of bands, color-coded running medians or running means of signal intensity (normalized and log-scaled) in different fragments are displayed; the window size of the running medians or running means increases from top to bottom. A corresponding colour legend is added in an extra plot.
This function provides some 4C-seq quality statistics based on the experiment's read distribution throughout the genome. getReadDistribution calculates the number of total reads, cis to overall ratio of reads, and the percentage of covered fragment ends within a certain distance around the experiment's viewpoint. Reference values for high-quality experiments, as provided by van de Werken et al, 2012, are more than one million reads total, a cis to overall ratio of more than 40% and a large fraction of covered fragment ends in the viewpoint's vicinity.
This function is a small convenience function that reads in a prepared file with restriction enzyme sequence names and sequences. giveEnzymeSequence then provides restriction enzyme sequences for the example enzymes listed in van de Werken et al's 4Cseqpipe data base.
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