# Spike-in calibration for cell-free MeDIP

## Documentation for package ‘spiky’ version 1.0.0

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

## Help Pages

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.