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. |