BED2txDb
(Package: RNAprobR) :
Bedgraph to TranscriptDb object
Function to transform BED format file to Bioconductor TranscriptDb object
● Data Source:
BioConductor
● Keywords:
● Alias: BED2txDb
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GR2norm_df
(Package: RNAprobR) :
Export normalized GRanges object to data frame
Function to make data frame out of GRanges output of normalizing functions (dtcr(), slograt(), swinsor(), compdata()) for all or a set of chosen transcripts in the file.
● Data Source:
BioConductor
● Keywords:
● Alias: GR2norm_df
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bam2bedgraph
(Package: RNAprobR) :
Function converts bam file to bedgraph by counting number of reads starting at each position (termination counts)
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● Data Source:
BioConductor
● Keywords:
● Alias: bam2bedgraph
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Function importing data from bedgraph format compatible with UCSC Genome Browser to norm_GR data frame. Warning: Compatible only with bedgraph files generated by norm2bedgraph function (bedgraph needs to have 2 tracks, first for plus strand, second for minus strand). May be used for transforming normalized data to another different annotation sets.
● Data Source:
BioConductor
● Keywords:
● Alias: bedgraph2norm
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comp
(Package: RNAprobR) :
Arranging information from GRanges produced by readsamples() on
comp() takes as input euc_GR GRanges object produced by readsamples() and produces Comp_GR GRanges.
● Data Source:
BioConductor
● Keywords:
● Alias: comp
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compdata
(Package: RNAprobR) :
Create or extend norm_GR GRanges using Comp_GR GRanges
Add metadata present in GRanges made by comp() function (termination count (TC), termination-coverage ratio (TCR), coverage (Cover) and priming count (PC)) to GRanges made by normalizing functions (dtcr(), slograt(), swinsor(), compdata()).
● Data Source:
BioConductor
● Keywords:
● Alias: compdata
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If for a given fragment the number of observed unique barcodes is equal to the total barcode complexity (all combinations of barcodes are associated with a given fragment), then the readsamples function assignes infinite EUC. This can be corrected by the function correct_oversaturation(). By comparing observed read counts with EUCs for other fragments it calculates the correction factor. Then, for the oversaturated fragments it multiplies the observed read counts by the correction factor to estimate EUC. The assumption behind this correction is that fragments have similar rate of PCR duplicates production.
● Data Source:
BioConductor
● Keywords:
● Alias: correct_oversaturation
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dtcr
(Package: RNAprobR) :
Calculate deltaTCR.
Performs deltaTCR (dtcr) normalization given control and treated GRanges generated by comp() function.
● Data Source:
BioConductor
● Keywords:
● Alias: dtcr
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k2n_calc
(Package: RNAprobR) :
Calculate number of Estimated Unique Counts (EUC's)
Function calculates EUC's for each number of observed barcodes accounting for differential ligation probability of different barcodes. Function k2n_calc() writes file with a vector in which an i-th element is an estimated unique count given observing i unique barcodes.
● Data Source:
BioConductor
● Keywords:
● Alias: k2n_calc
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norm2bedgraph
(Package: RNAprobR) :
Exporting data in norm_df data frame (product of dtcr, slograt and
Function converts annotation from transcript to genomic coordinates and creates two-track bedgraph file (one track for each strand)
● Data Source:
BioConductor
● Keywords:
● Alias: norm2bedgraph
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