biscuiteer 1.14.0
knitr::opts_chunk$set( warning=FALSE, message=FALSE )
biscuiteer is package to process output from
biscuit into
bsseq objects. It includes a number
of features, such as VCF header parsing, shrunken M-value calculations (which
can be used for compartment inference), and age inference. However, the task of
locus- and region-level differential methylation inference is delegated to
other packages (such as dmrseq).
From Bioconductor,
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("biscuiteer")A development version is available on GitHub and can be installed via:
biscuiteer can load either headered or header-free BED files produced from
biscuit vcf2bed or biscuit mergecg. In either case, a VCF file is needed
when loading biscuit output. For practical purposes, only the VCF header is
for biscuiteer. However, it is encouraged that the user keep the entire VCF,
as biscuit can be used to call SNVs and allows for structural variant
detection in a similar manner to typical whole-genome sequencing tools.
Furthermore, biscuit records the version of the software and the calling
arguments used during processing the output VCF, which allows for better
reproducibility.
NOTE: Both the input BED and VCF files must be tabix’ed before being input to
biscuiteer. This can be done by running bgzip biscuit_output.xxx followed by
tabix -p xxx biscuit_output.xxx.gz, where xxx is either bed or vcf.
Data can be loaded using the readBiscuit function in biscuiteer:
## Loading required package: biscuiteerData## Loading required package: ExperimentHub## Loading required package: BiocGenerics##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:stats':
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## pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: AnnotationHub## Loading required package: BiocFileCache## Loading required package: dbplyr## Warning: replacing previous import 'utils::findMatches' by
## 'S4Vectors::findMatches' when loading 'AnnotationDbi'## Loading biscuiteerData.## Loading required package: bsseq## Loading required package: GenomicRanges## Loading required package: stats4## Loading required package: S4Vectors##
## Attaching package: 'S4Vectors'## The following object is masked from 'package:utils':
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## I, expand.grid, unname## Loading required package: IRanges## Loading required package: GenomeInfoDb## Loading required package: SummarizedExperiment## Loading required package: MatrixGenerics## Loading required package: matrixStats##
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## rowWeightedSds, rowWeightedVars## Loading required package: Biobase## Welcome to Bioconductor
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## cache## ## ## ## Warning: replacing previous import 'BiocParallel::bpstart' by
## 'QDNAseq::bpstart' when loading 'biscuiteer'orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz",
package="biscuiteer")
orig_vcf <- system.file("extdata", "MCF7_Cunha_header_only.vcf.gz",
package="biscuiteer")
bisc <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf,
merged = FALSE)## Checking /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15.bed.gz for import...## Extracting sample names from /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_header_only.vcf.gz...## /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15.bed.gz does not have a header. Using VCF file header information to help set column names.## Assuming unmerged data. Checking now... ...The file might be alright. Double check if you're worried.
## /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15.bed.gz has 254147 indexed loci.
## /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15.bed.gz looks valid for import.
## Reading unmerged input from /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15.bed.gz...
## Excluding CpG sites with uniformly zero coverage...
## Loaded /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15.bed.gz. Creating bsseq object......Done!Metadata from the biscuit output can be viewed via:
## CharacterList of length 3
## [["Reference genome"]] hg19.fa
## [["Biscuit version"]] 0.1.3.20160324
## [["Invocation"]] biscuit pileup -r /primary/vari/genomicdata/genomes/hg19/hg1...If further information about the VCF header is desired,
## class: VCFHeader
## samples(1): MCF7_Cunha
## meta(5): fileformat reference source contig program
## fixed(1): FILTER
## info(3): NS CX N5
## geno(7): GT DP ... GL GQIn the instance where you have two separate BED files that you would like to
analyze in a single bsseq object, you can combine the files using unionize,
which is a wrapper around the BiocGenerics function, combine.
shuf_bed <- system.file("extdata", "MCF7_Cunha_chr11p15_shuffled.bed.gz",
package="biscuiteer")
shuf_vcf <- system.file("extdata",
"MCF7_Cunha_shuffled_header_only.vcf.gz",
package="biscuiteer")
bisc2 <- readBiscuit(BEDfile = shuf_bed, VCFfile = shuf_vcf,
merged = FALSE)## Checking /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15_shuffled.bed.gz for import...## Extracting sample names from /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_shuffled_header_only.vcf.gz...## /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15_shuffled.bed.gz does not have a header. Using VCF file header information to help set column names.## Assuming unmerged data. Checking now... ...The file might be alright. Double check if you're worried.
## /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15_shuffled.bed.gz has 254147 indexed loci.
## /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15_shuffled.bed.gz looks valid for import.
## Reading unmerged input from /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15_shuffled.bed.gz...
## Excluding CpG sites with uniformly zero coverage...
## Loaded /tmp/RtmpmCDVpa/Rinst3f214f498a58bb/biscuiteer/extdata/MCF7_Cunha_chr11p15_shuffled.bed.gz. Creating bsseq object......Done!The epiBED file format provides an easy way to analyze read- or fragment-level
methylation and genetic information at the same time. readEpibed provides
functionality for parsing the RLE strings found in the epiBED file into a
GRanges object for analysis in R.
NOTE: The input file must be bgzip’ed and tabix’ed.
epibed.nome <- system.file("extdata", "hct116.nome.epibed.gz", package="biscuiteer")
epibed.bsseq <- system.file("extdata", "hct116.bsseq.epibed.gz", package="biscuiteer")
epibed.nome.gr <- readEpibed(epibed = epibed.nome, genome = "hg19", chr = "chr1")## Decoding RLE and converting to GRanges## Collapsing to fragment level## This will take some time if a large region is being analyzed## Decoding RLE and converting to GRanges## Collapsing to fragment level## This will take some time if a large region is being analyzedA handful of analysis paths are available in biscuiteer, including A/B
comparment inference, age estimation from WGBS data, hypermethylation of
Polycomb Repressor Complex (PRC) binding sites, and hypomethylation of
CpG-poor “partially methylated domains” (PMDs).
When performing A/B compartment inference, the goal is to have something that
has roughly gaussian error. getLogitFracMeth uses Dirichlet smoothing to turn
raw measurements into lightly moderated, logit-transformed methylated-fraction
estimates, which can the be used as inputs to
compartmap
reg <- GRanges(seqnames = rep("chr11",5),
strand = rep("*",5),
ranges = IRanges(start = c(0,2.8e6,1.17e7,1.38e7,1.69e7),
end= c(2.8e6,1.17e7,1.38e7,1.69e7,2.2e7))
)
frac <- getLogitFracMeth(bisc, minSamp = 1, r = reg)
frac## GRanges object with 5 ranges and 1 metadata column:
## seqnames ranges strand | MCF7_Cunha
## <Rle> <IRanges> <Rle> | <numeric>
## [1] chr11 0-2800000 * | 1.340682
## [2] chr11 2800000-11700000 * | 0.575875
## [3] chr11 11700000-13800000 * | 1.162989
## [4] chr11 13800000-16900000 * | 0.581874
## [5] chr11 16900000-22000000 * | 0.442985
## -------
## seqinfo: 1 sequence from an unspecified genome; no seqlengthsbiscuiteer has the functionalitity to guess the age of the sample(s) provided
using the Horvath-style “clock” models (see
Horvath, 2013
for more information).
NOTE: The prediction accuracy of this function is entirely dependent on the parameters set by the user. As such, the defaults (as shown in the example below) should only be used as a starting point for exploration by the user.
NOTE: Please cite the appropriate papers for the epigenetic “clock” chosen:
* For horvath or horvathshrunk
* Horvath, Genome Biology, 2013
* For hannum
* Hannum et al., Molecular Cell, 2013
* For skinandblood
* Horvath et al., Aging, 2018
## Assessing coverage across age-associated regions...## You have NAs. Change `padding` (15), `minCovg` (5), `useHMMI`, and/or `useENSR`. You have 702 positions in coverage matrix (regions x samples) with less than 5 minCovg. This represents 99.43 % missing data## $call
## WGBSage(comb, "horvath")
##
## $droppedSamples
## NULL
##
## $droppedRegions
## NULL
##
## $intercept
## [1] 0.6955073
##
## $methcoefs
## GRanges object with 353 ranges and 3 metadata columns:
## seqnames ranges strand | MCF7_Cunha
## <Rle> <IRanges> <Rle> | <numeric>
## chr1:1168022-1168051 chr1 1168022-1168051 * | NA
## chr1:19746550-19746579 chr1 19746550-19746579 * | NA
## chr1:23858021-23858050 chr1 23858021-23858050 * | NA
## chr1:32084950-32084979 chr1 32084950-32084979 * | NA
## chr1:32687553-32687582 chr1 32687553-32687582 * | NA
## ... ... ... ... . ...
## chr22:42322132-42322161 chr22 42322132-42322161 * | NA
## chr22:43506007-43506036 chr22 43506007-43506036 * | NA
## chr22:46449447-46449476 chr22 46449447-46449476 * | NA
## chr22:46450093-46450122 chr22 46450093-46450122 * | NA
## chr22:50968329-50968358 chr22 50968329-50968358 * | NA
## MCF7_Cunha_shuffled coefs
## <numeric> <numeric>
## chr1:1168022-1168051 NA 0.6285003
## chr1:19746550-19746579 NA 0.0138482
## chr1:23858021-23858050 NA -0.1663978
## chr1:32084950-32084979 NA 0.0989124
## chr1:32687553-32687582 NA 0.0358242
## ... ... ...
## chr22:42322132-42322161 NA 0.7000011
## chr22:43506007-43506036 NA 0.1270524
## chr22:46449447-46449476 NA -0.1662689
## chr22:46450093-46450122 NA -0.0912389
## chr22:50968329-50968358 NA 0.1373155
## -------
## seqinfo: 22 sequences from hg19 genome
##
## $age
## MCF7_Cunha MCF7_Cunha_shuffled
## 33.18896 34.88742