NEWS

RiboProfiling 1.7.2

Corrected a bug in utils.R, readStartCov1Aln function. normRange(listReadStartCov, fixedInterval), in case ixReverse null

For the vignette the example bam files have been down-sampled and added to the extdata folder
Changed the vignette accordingly

replaced IRanges::as.table since it is not exported by IRanges anymore, with as.table
motifSize in countShiftReads and codonInfo can be only 3, 6 or 9
in countShiftReads and codonInfo, motifs of size 6 or 9 correspond to overalpping windows, sliding 1 codon at a time
in countShiftReads, for motifSize = 6, the P-site is the first codon of the 2 it means that only the reads of the 1st codon in the 2 codon-motif are counted
in countShiftReads, for motifSize = 9, the P-site is the second codon of the 3 it means that only the reads of the 2nd codon in the 3 codon-motif are counted
adapted the RiboProfiling.Rnw to explain the treatment of motifs of codons (1, 2, or 3) as opposed to the previous treatment of unique codons.
changed S4Vectors::elementLengths to S4Vectors::elementNROWS in riboSeqFromBAM, aroundPromoter

replaced GenomicRanges::assays since it is not exported by GenomicRanges anymore, by SummarizedExperiment::assays, and importFrom

replaced GenomicRanges::assays since it is not exported by GenomicRanges anymore, by assays

function "codonInfo" modified optimized for motifs of 1 or 2 consecutive codons
getCodons (utils), countShiftReads, and codonInfo functions modified it allows to look at sequence motifs not only for codons (3 nucleotides) but for other sizes as well motifSize parameter has been added to these functions to specify the number of nucleotides on which to compute usage and coverage.
function "readsToReadStart" replaced by "readsToStartOrEnd" this new function focuses not only the read 5' (start) but also the read 3' (end)
In riboSeqFromBAM added a parameter offsetStartEnd. It specifies if the offset is to be computed on the 5' or 3' of the read.

Non-null coverage values define the percentage of best expressed CDSs.
New function: readsToReadStart - it builds the GRanges object of the read start genomic positions
Acronym BAM used instead of bam
Correction of read start coverage (readStartCov) for the reverse strand
Title in Description in Title Case
Typos corrections in vignette.
Style inconsistencies solved: = replaced by <- outside named arguments No space around “=” when using named arguments to functions. This: somefunc(a=1, b=2) spaces around binary operators a space after all commas use of camelCase for both variable and function names ORFrelativePos -> orfRelativePos
Replaced 1:length(x) by seq_len(length(x))
Replaced 1:nrow(x) by seq_len(NROW(x))
Replaced trailing white spaces with this command: 'find . -type f -path './*R' -exec perl -i -pe 's/ +$//' {} \;'
countsPlot, histMatchLength, plotSummarizedCov: no longer print directly the graphs. Instead they return a list of graphs.
Replaced 'class()' tests by 'inherits' or 'is'.
The codonPCA function no longer prints the PCA graphs sequantially. The 5 PCA graphs are returned, together with the PCA scores.
New function printPCA prints the 5 PCA plots produced by codonPCA.
A BAM file is now available in the inst/extdata ctrl_sample.bam. It is used in the testriboSeqFromBAM testthat

Modified the vignette: small corrections of the explanatory text.
Added testthat tests for the following functions: test-aroundPromoter.R, test-riboSeq_fromBAM.R, test-readStartCov.R
Introduced the 4 spaces tabulation
Reduced the percentage of lines > 80 characters to 2%
Added imports in the Namespace for the proposed packages or methods
New R version: 3.2.2 and bioconductor packages update

Added biocViews: Sequencing, Coverage, Alignment, QualityControl, Software, PrincipalComponent
Added testthat tests for the following functions: test-aroundPromoter.R, test-riboSeq_fromBAM.R, test-readStartCov.R
Introduced the 4 spaces tabulation
Reduced the percentage of lines > 80 characters to 2%
Added imports in the Namespace for the proposed packages or methods v.0.99.0 Initial release.