An R package for analysis of massive parallel sequencing based RNA structure probing data


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Documentation for package ‘RNAprobR’ version 1.12.0

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bam2bedgraph Function converts bam file to bedgraph by counting number of reads starting at each position (termination counts). It creates two-track bedgraph file (one track for each strand).
BED2txDb Bedgraph to TranscriptDb object
bedgraph2norm Import bedgraph to GRanges
comp Arranging information from GRanges produced by readsamples() on per position (nucleotide) basis.
compdata Create or extend norm_GR GRanges using Comp_GR GRanges
correct_oversaturation Correcting EUC of oversaturated fragments.
dtcr Calculate deltaTCR.
GR2norm_df Export normalized GRanges object to data frame
k2n_calc Calculate number of Estimated Unique Counts (EUC's) corresponding to given number of observed unique barcodes.
norm2bedgraph Exporting data in norm_df data frame (product of dtcr, slograt and swinsor) to bedgraph format compatible with UCSC Genome Browser
norm_df2GR Function to convert norm_df data frame (product of GR2norm_df()) to GRanges.
plotReads Plotting ranges from GRanges
plotRNA Plot normalized values over transcript positions
readsamples Import of tables prepared by Galaxy workflow to R environment
slograt Smooth Log2-ratio
swinsor Smooth Winsorization
swinsor_vector Smooth Winsor Normalization
winsor Winsor normalization with fitting to <0,1> range.