RNA Coverage-Shape-Based Quality Control Metrics

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Documentation for package ‘RNAshapeQC’ version 0.99.10

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS

Help Pages

.build_pileupExon	Core helper to build exon-only pileup
combine_vecObj	Combine vectors as a matrix from objects
compute_DIIwt	Core helper to compute a degraded/intact index using gene weight
compute_DR	Core helper to compute decay rate
compute_MCD	Core helper to compute a mean coverage depth
compute_SOI	Core helper to compute a suboptimal/optimal index
compute_wCV	Core helper to compute a window coefficient of variation
construct_pileup	Construct a per-gene pileup from BAM files (for single-study or multi-study)
extract_RData	Extract an object from .RData
filter_lowExpGenes	Filter low expressed genes
gen_DR	Get a decay rate for genes and samples (for a single gene)
gen_MCD	Get a mean coverage depth for genes and samples (for a single gene)
gen_wCV	Get a window coefficient of variation for genes and samples (for a single gene)
get_DIIhc	Get a degraded/intact index for samples using hierarchical clustering
get_DIIwt	Get a degraded/intact index for samples using gene weight
get_DR	Get a decay rate for genes and samples (for a genelist)
get_MCD	Get a mean coverage depth for genes and samples (for a genelist)
get_pileupExon	Get a focused pileup of exon location (for single-study)
get_SOI	Get a suboptimal/optimal index for samples
get_wCV	Get a window coefficient of variation for genes and samples (for a genelist)
plot_DIIwt	Plot degraded/intact index outputs
plot_GBC	Plot gene body coverage
plot_GBCos	Plot gene body coverage with optimal samples
plot_SOI	Plot suboptimal/optimal index outputs
TOY_mrna_mat	Toy mRNA-seq-like dataset for RNAshapeQC (matrix input)
TOY_mrna_se	Toy mRNA-seq-like dataset for RNAshapeQC (SE input)
TOY_total_mat	Toy total RNA-seq-like dataset for RNAshapeQC (matrix input)
TOY_total_se	Toy total RNA-seq-like dataset for RNAshapeQC (SE input)