Spike-in calibration for cell-free MeDIP

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Documentation for package ‘spiky’ version 1.2.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

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add_frag_info	decode fragment identifiers for spike-in standards
bam_to_bins	create a tiled representation of a genome from the BAM/CRAM file
bin_pmol	Binned estimation of picomoles of DNA present in cfMeDIP assays
covg_to_df	reshape 'scan_spiked_bam' results into data.frames for model_glm_pmol
dedup	spike-in counts for two samples, as a wide data.frame
find_spike_contigs	find spike-in seqlevels in an object 'x', where !is.null(seqinfo(x))
genbank_mito	various mitochondrial genomes sometimes used as endogenous spike-ins
generate_spike_fasta	for CRAM files, a FASTA reference is required to decode; this builds that
get_base_name	refactored out of rename_spikes and rename_spike_seqlevels
get_binned_coverage	tabulate read coverage in predefined bins
get_merged_gr	get a GRanges of (by default, standard) chromosomes from seqinfo
get_spiked_coverage	tabulate coverage across assembly and spike contig subset in natural order
get_spike_depth	get the (max, median, or mean) coverage for spike-in contigs from a BAM/CRAM
kmax	simple contig kmer comparisons
kmers	oligonucleotideFrequency, but less letters and more convenient.
methylation_specificity	compute methylation specificity for spike-in standards
model_bam_standards	Build a Bayesian additive model from spike-ins to correct bias in *-seq
model_glm_pmol	Build a generalized linear model from spike-ins to correct bias in cfMeDIP
parse_spike_UMI	parse out the forward and reverse UMIs and contig for a BED/BAM
phage	lambda and phiX phage sequences, sometimes used as spike-ins
plot-method	A handful of methods that I've always felt were missing
predict_pmol	predict picomoles of DNA from a fit and read counts (coverage)
process_spikes	QC, QA, and processing for a new spike database
rename_spikes	for BAM/CRAM files with renamed contigs, we need to rename 'spike' rows
rename_spike_seqlevels	for spike-in contigs in GRanges, match to standardized spike seqlevels
scan_genomic_contigs	scan genomic contigs in a BAM/CRAM file
scan_methylation_specificity	tabulate methylation specificity for multiple spike-in BAM/CRAM files
scan_spiked_bam	pretty much what it says: scan standard chroms + spike contigs from a BAM
scan_spike_contigs	pretty much what it says: scan spike contigs from a BAM or CRAM file
scan_spike_counts	run spike_counts on BAM/CRAM files and shape the results for model_glm_pmol
seqinfo_from_header	create seqinfo (and thus a standard chromosome filter) from a BAM/CRAM header
spike	spike-in contig properties for Sam's cfMeDIP spikes
spike_bland_altman_plot	Bland-Altman plot for cfMeDIP spike standards
spike_counts	use the index of a spiked BAM/CRAM file for spike contig coverage
spike_cram_counts	spike-in counts, as a long data.frame
spike_read_counts	spike-in counts, as a long data.frame
spiky-methods	A handful of methods that I've always felt were missing
ssb_res	scan_spiked_bam results from a merged cfMeDIP CRAM file (chr22 and spikes)
testGR	a test GRanges with UMI'ed genomic sequences used as controls
tile_bins	Tile the assembly-based contigs of a merged assembly/spike GRanges.