Spike-in calibration for cell-free MeDIP


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Documentation for package ‘spiky’ version 1.2.0

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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.