NEWS.md
merge_rse_metrics() can now also handle ERCCsumLogErr. Note that its an approximation given properties of logarithms. To compute the actual correct values, you would need access to the original output ERCC quantification output files.skipLines argument to junctionCount to resolve https://github.com/LieberInstitute/jaffelab/issues/8.cleaningY() now supports NAs in the input y.googledrive_csv() function for uploading CSV files to Google Drive. It used to be internal code of lab_presenters() but could be more useful outside of it.lab_presenters() function for randomizing lab presenters. Could also be used for randomizing the lab snacks rotation.NEWS.md file to track changes to the package, thus replacing the existing NEWS file.pkgdown::build_site() version for the documentation of the package.NEW FEATURES
agePlotter(), cleaningY(), getR2(), edge.pvalue() and noted that junctionCount() is missing a full example.NEW FEATURES
merge_rse_metrics() that merges some of the sample metadata metrics for samples that were sequenced in more than one lane. Useful for the RangedSummarizedExperiment objects we typically produce for RNA-seq experiments at the Jaffe lab.NEW FEATURES
granges_to_ucsc() function, which is the reverse of ucsc_to_granges().NEW FEATURES
corner() which takes head of rows and columns of objectsSIGNIFICANT USER-VISIBLE CHANGES
agePlotter(): changed how the X-axis ticks and range are made for the prenatal samples.NEW FEATURES
ucsc_to_granges() function that converts a character vector of coordinates from the UCSC genome browser to a GRanges object.SIGNIFICANT USER-VISIBLE CHANGES
agePlotter() is now more flexible and can handle up a vector of pointColor and lineColor. Also, the breaks are now flexible and support more scenarios (you need at least 3 groups).NEW FEATURES
expression_cutoff() which finds suggested expression cutoffs for an RPKM matrix.BUG FIXES
cleaningY(). This is after Stephen Semick and Emily Burke reported issues with the function.SIGNIFICANT USER-VISIBLE CHANGES
coverage_bwtool() to the recount.bwtool package.NEW FEATURES
coverage_bwtool() for computing coverage matrices using bwtool for a user-specified list of bigWig files and a user-specified phenotype table. It’s heavily based on recount.bwtoolSIGNIFICANT USER-VISIBLE CHANGES
junctionCount() uses check.names = FALSE when calling DataFrame(). Related to a bug Badoi Phan reported.BUG FIXES
junctionCount() work for single-end libraries. Still need to trace why ? are being added as the strand.SIGNIFICANT USER-VISIBLE CHANGES
splitit() since it’s available in rafalib.