MMAPPR2 1.12.0
You’ll need BAM file(s) for your wild-type pool, BAM file(s) for your mutant pool, and the reference genome for your species in fasta format. We recommend that each pool contain at least 20 individuals to ensure a good number of recombinations to measure.
MMAPPR2 depends on two system tools to function: Samtools and VEP. Both must be installed and in the PATH to be found by the appropriate functions.
Instructions to install samtools can be found at https://github.com/samtools/samtools and installation instructions are in the INSTALL file included with samtools.
You’ll need Ensembl VEP, which you can install like this, replacing my_species with
your species (e.g., danio_rerio):
git clone https://github.com/Ensembl/ensembl-vep.git
cd ensembl-vep
perl INSTALL.pl -a ac -s {my_species}This installs the most recent VEP and allows you to create a cache for your desired species, which is what MMAPPR2 expects by default.
If you depart from the installation shown here, or if things don’t go smoothly, see Ensembl’s instructions
and make sure any differences are accounted for in the
VEPFlags object.
Note: If you have any trouble installing VEP, using their Docker image may save you a lot of hassle.
Note: We have found that R sometimes has issues finding VEP, especially when perlbrew is used. If you encounter errors at the path to your perl installation to the .Rprofile file. For example:
Sys.setenv(PATH=paste("/Path/to/Perlbrew", Sys.getenv("PATH"), sep=":"))For our example, we will use just the golden gene from the GRCz11 zebrafish reference genome.
Here we also configure the VEPFlags object to use our example fasta and GTF files. See below for more info.
Make sure your reference genome is the same you’ll use with VEP! This will be the most recent assembly available on Ensembl unless you customize. You should use the same genome in aligning your sequencing data as well.
BiocParallel::register(BiocParallel::MulticoreParam()) ## see below for explanation of BiocParallel
library(MMAPPR2, quietly = TRUE)
library(MMAPPR2data, quietly = TRUE)
library(Rsamtools, quietly = TRUE)##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:MMAPPR2':
##
## species, species<-## The following objects are masked from 'package:stats':
##
## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
##
## Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
## as.data.frame, basename, cbind, colnames, dirname, do.call,
## duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
## lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
## pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
## tapply, union, unique, unsplit, which.max, which.min##
## Attaching package: 'S4Vectors'## The following objects are masked from 'package:base':
##
## I, expand.grid, unname##
## Attaching package: 'IRanges'## The following object is masked from 'package:MMAPPR2':
##
## distance##
## Attaching package: 'Biostrings'## The following object is masked from 'package:base':
##
## strsplit# This is normally configured automatically:
vepFlags <- ensemblVEP::VEPFlags(flags = list(
format = 'vcf', # <-- this is necessary
vcf = FALSE, # <-- as well as this
species = 'danio_rerio',
database = FALSE, # <-- these three arguments allow us to run VEP offline,
fasta = goldenFasta(), # <-╯| which you probably won't need
gff = goldenGFF(), # <------╯
filter_common = TRUE,
coding_only = TRUE # assuming RNA-seq data
))
param <- MmapprParam(refFasta = goldenFasta(),
wtFiles = exampleWTbam(),
mutFiles = exampleMutBam(),
species = 'danio_rerio',
vepFlags = vepFlags, ## optional
outputFolder = tempOutputFolder()) ## optional## NOTE: genome 'danio_rerio' already exists, not overwritingWith parameters set, running the pipeline should be as simple as the following:
mmapprData <- mmappr(param)## ------------------------------------## -------- Welcome to MMAPPR2 --------## ------------------------------------## Start time: 2022-12-09 17:09:08## Output folder: /tmp/RtmpCIuUPJ/Rbuild3cdc05d4de929/MMAPPR2/vignettes//tmp/RtmpW4Lvjw/mmappr2_2022-12-09_17:09:08## Reading BAM files and generating Euclidean distance data...## Generating optimal Loess curves for each chromosome...## Identifying chromosome(s) harboring linkage region...## Peak regions succesfully identified## Refining peak characterization using SNP resampling...## Generating, analyzing, and ranking candidate variants...## Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 1 out-of-bound range located on sequence 18.
## Note that ranges located on a sequence whose length is unknown (NA) or
## on a circular sequence are not considered out-of-bound (use
## seqlengths() and isCircular() to get the lengths and circularity flags
## of the underlying sequences). You can use trim() to trim these ranges.
## See ?`trim,GenomicRanges-method` for more information.## Warning in .Call(.make_vcf_geno, filename, fixed, names(geno), as.list(geno), :
## converting NULL pointer to R NULL## Writing output plots and tables...##
## End time: 2022-12-09 17:09:21## MMAPPR2 runtime: 12.58076 secsThe MMAPPR2 pipeline can also be run a step at a time:
md <- new('MmapprData', param = param) ## calculateDistance() takes a MmapprData object
postCalcDistMD <- calculateDistance(md)
postLoessMD <- loessFit(postCalcDistMD)
postPrePeakMD <- prePeak(postLoessMD)
postPeakRefMD <- peakRefinement(postPrePeakMD)
postCandidatesMD <- generateCandidates(postPeakRefMD)## Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 1 out-of-bound range located on sequence 18.
## Note that ranges located on a sequence whose length is unknown (NA) or
## on a circular sequence are not considered out-of-bound (use
## seqlengths() and isCircular() to get the lengths and circularity flags
## of the underlying sequences). You can use trim() to trim these ranges.
## See ?`trim,GenomicRanges-method` for more information.## Warning in .Call(.make_vcf_geno, filename, fixed, names(geno), as.list(geno), :
## converting NULL pointer to R NULLoutputMmapprData(postCandidatesMD)If the pipeline fails midway, the MmapprData object is saved, which you can then load
and use for inspection and debugging:
## Contents of output folder:
cat(paste(system2('ls', outputFolder(param(mmapprData)), stdout = TRUE)), sep = '\n')## 18.tsv
## genome_plots.pdf
## mmappr2.log
## mmappr_data.RDS
## peak_plots.pdfmdFile <- file.path(outputFolder(param(mmapprData)), 'mmappr_data.RDS')
md <- readRDS(mdFile)
md## MmapprData object with following slots:
## param:
## MmapprParam object with following values:
## Reference fasta file:
## /home/biocbuild/bbs-3.16-bioc/R/library/MMAPPR2data/extdata/slc24a5.fa.gz
## wtFiles:
## BamFileList of length 1
## names(1): wt.bam
## mutFiles:
## BamFileList of length 1
## names(1): mut.bam
## vepFlags:
## class: VEPFlags
## flags(6): format, species, ..., filter_common, coding_only
## version: 105
## scriptPath:
## refGenome:
## GmapGenome object
## genome: danio_rerio
## directory: /home/biocbuild/.local/share/gmap
## Other parameters:
## species
## danio_rerio
## distancePower
## 4
## peakIntervalWidth
## 0.95
## minDepth
## 10
## homozygoteCutoff
## 0.95
## minBaseQuality
## 20
## minMapQuality
## 30
## loessOptResolution
## 0.001
## loessOptCutFactor
## 0.1
## naCutoff
## 0
## outputFolder
## /tmp/RtmpW4Lvjw/mmappr2_2022-12-09_17:09:08
## fileAggregation
## sum
## distance:
## Contains Euclidian distance data for 1 sequence(s)
## and Loess regression data for 1 of those
## Memory usage = 1 MB
## peaks:
## 18: start = -158, end = 14089
## Density function calculated
## candidates:
## $`18`
## GRanges object with 12 ranges and 30 metadata columns:
## seqnames ranges strand | Allele Consequence
## <Rle> <IRanges> <Rle> | <character> <character>
## 18:5744_A/C 18 5744 * | C missense_variantIf everything goes well you should be able to track down your mutation using the candidates slot of your MmapprData
object or by looking at files in the output folder:
head(candidates(mmapprData)$`18`, n=2)## GRanges object with 2 ranges and 30 metadata columns:
## seqnames ranges strand | Allele Consequence
## <Rle> <IRanges> <Rle> | <character> <character>
## 18:5744_A/C 18 5744 * | C missense_variant
## 18:5736_T/C 18 5736 * | C missense_variant
## IMPACT SYMBOL Gene Feature_type
## <character> <character> <character> <character>
## 18:5744_A/C MODERATE ENSDARG00000024771 ENSDARG00000024771 Transcript
## 18:5736_T/C MODERATE ENSDARG00000024771 ENSDARG00000024771 Transcript
## Feature BIOTYPE EXON INTRON
## <character> <character> <character> <character>
## 18:5744_A/C ENSDART00000033574 protein_coding 6/9 <NA>
## 18:5736_T/C ENSDART00000033574 protein_coding 6/9 <NA>
## HGVSc HGVSp cDNA_position CDS_position
## <character> <character> <character> <character>
## 18:5744_A/C <NA> <NA> 940 880
## 18:5736_T/C <NA> <NA> 932 872
## Protein_position Amino_acids Codons Existing_variation
## <character> <character> <character> <character>
## 18:5744_A/C 294 S/R Agc/Cgc <NA>
## 18:5736_T/C 291 L/P cTa/cCa <NA>
## DISTANCE STRAND FLAGS SYMBOL_SOURCE HGNC_ID
## <character> <character> <character> <character> <character>
## 18:5744_A/C <NA> 1 <NA> <NA> <NA>
## 18:5736_T/C <NA> 1 <NA> <NA> <NA>
## SOURCE FREQS CLIN_SIG SOMATIC PHENO
## <character> <character> <character> <character> <character>
## 18:5744_A/C slc24a5.gff.gz <NA> <NA> <NA> <NA>
## 18:5736_T/C slc24a5.gff.gz <NA> <NA> <NA> <NA>
## slc24a5.gff.gz peakDensity
## <character> <numeric>
## 18:5744_A/C <NA> 5.98560e-05
## 18:5736_T/C <NA> 5.92124e-05
## -------
## seqinfo: 1 sequence from genomeoutputTsv <- file.path(outputFolder(param(mmapprData)), '18.tsv')
cat(paste(system2('head', outputTsv, stdout = TRUE)), sep = '\n')## Position Symbol Impact Consequence DensityScore Allele AminoAcid Feature
## 5744 ENSDARG00000024771 MODERATE missense_variant 5.9856022103958e-05 C S/R ENSDART00000033574
## 5736 ENSDARG00000024771 MODERATE missense_variant 5.92123503476737e-05 C L/P ENSDART00000033574
## 5494 ENSDARG00000024771 HIGH stop_gained 5.85645259563949e-05 G Y/* ENSDART00000033574
## 5706 ENSDARG00000024771 MODERATE missense_variant 5.64958520790885e-05 C I/T ENSDART00000033574
## 5601 ENSDARG00000024771 MODERATE missense_variant 5.07691258419513e-05 C C/S ENSDART00000033574
## 4117 ENSDARG00000024771 MODERATE missense_variant 3.27869668698596e-05 C V/L ENSDART00000033574
## 7197 ENSDARG00000024771 MODERATE missense_variant 2.73823317888854e-05 C M/I ENSDART00000033574
## 7244 ENSDARG00000024771 MODERATE missense_variant 2.23137418196834e-05 C V/A ENSDART00000033574
## 7336 ENSDARG00000024771 MODERATE missense_variant 1.11888913939222e-05 C I/L ENSDART00000033574MMAPPR2 uses the ensemblVEP Bioconductor package to predict the effect of variants in the peak region.
To customize this process, you’ll need to configure a VEPFlags object. Look at Ensembl’s website for script options. You can configure the VEPFlags object like this:
library(ensemblVEP, quietly = TRUE)##
## Attaching package: 'MatrixGenerics'## The following objects are masked from 'package:matrixStats':
##
## colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
## colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
## colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
## colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
## colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
## colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
## colWeightedMeans, colWeightedMedians, colWeightedSds,
## colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
## rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
## rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
## rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
## rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
## rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
## rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
## rowWeightedSds, rowWeightedVars## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.##
## Attaching package: 'Biobase'## The following object is masked from 'package:MatrixGenerics':
##
## rowMedians## The following objects are masked from 'package:matrixStats':
##
## anyMissing, rowMedians##
## Attaching package: 'VariantAnnotation'## The following object is masked from 'package:base':
##
## tabulate##
## Attaching package: 'ensemblVEP'## The following object is masked from 'package:Biobase':
##
## cache## The following object is masked from 'package:BiocStyle':
##
## outputvepFlags <- VEPFlags(flags = list(
### DEFAULT SETTINGS
format = 'vcf', # <-- this is necessary
vcf = FALSE, # <-- as well as this
species = 'danio_rerio',
database = FALSE,
cache = TRUE,
filter_common = TRUE,
coding_only = TRUE # assuming RNA-seq data
### YOU MAY FIND THESE INTERESTING:
# everything = TRUE # enables many optional analyses, such as Polyphen and SIFT
# per_gene = TRUE # will output only the most severe variant per gene
# pick = TRUE # will output only one consequence per variant
))MMAPPR2 simply uses the default bpparam registered. You can change this (for example, if BiocParallel isn’t working correctly) with the BiocParallel::register command. For example:
library(BiocParallel, quietly = TRUE)
register(SerialParam())
register(MulticoreParam(progressbar=TRUE))
registered()## $MulticoreParam
## class: MulticoreParam
## bpisup: FALSE; bpnworkers: 4; bptasks: 2147483647; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: TRUE
## bpexportglobals: TRUE; bpexportvariables: FALSE; bpforceGC: TRUE; bpfallback: TRUE
## bplogdir: NA
## bpresultdir: NA
## cluster type: FORK
##
## $SerialParam
## class: SerialParam
## bpisup: FALSE; bpnworkers: 1; bptasks: 0; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
## bpexportglobals: FALSE; bpexportvariables: FALSE; bpforceGC: FALSE; bpfallback: FALSE
## bplogdir: NA
## bpresultdir: NA
##
## $SnowParam
## class: SnowParam
## bpisup: FALSE; bpnworkers: 4; bptasks: 0; bpjobname: BPJOB
## bplog: FALSE; bpthreshold: INFO; bpstopOnError: TRUE
## bpRNGseed: ; bptimeout: NA; bpprogressbar: FALSE
## bpexportglobals: TRUE; bpexportvariables: TRUE; bpforceGC: FALSE; bpfallback: TRUE
## bplogdir: NA
## bpresultdir: NA
## cluster type: SOCKThe last param registered becomes the default.
The variant calling step requires a BiocStyle::Biocpkg("gmapR") GmapGenome, which is normally automatically generated from the refFasta parameter. If for some reason you want to generate your own, the process is like this:
refGenome <- gmapR::GmapGenome(goldenFasta(), name='slc24a5', create=TRUE)MMAPPR2, like its predecessor, was designed for and tested using RNA-Seq data. However, the principles at work should still apply for WGS data.
sessionInfo()## R version 4.2.2 (2022-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] BiocParallel_1.32.4 ensemblVEP_1.40.0
## [3] VariantAnnotation_1.44.0 SummarizedExperiment_1.28.0
## [5] Biobase_2.58.0 MatrixGenerics_1.10.0
## [7] matrixStats_0.63.0 Rsamtools_2.14.0
## [9] Biostrings_2.66.0 XVector_0.38.0
## [11] GenomicRanges_1.50.1 GenomeInfoDb_1.34.4
## [13] IRanges_2.32.0 S4Vectors_0.36.1
## [15] BiocGenerics_0.44.0 MMAPPR2data_1.12.0
## [17] MMAPPR2_1.12.0 BiocStyle_2.26.0
##
## loaded via a namespace (and not attached):
## [1] httr_1.4.4 sass_0.4.4 bit64_4.0.5
## [4] jsonlite_1.8.4 bslib_0.4.1 assertthat_0.2.1
## [7] BiocManager_1.30.19 VariantTools_1.40.0 BiocFileCache_2.6.0
## [10] blob_1.2.3 BSgenome_1.66.1 GenomeInfoDbData_1.2.9
## [13] yaml_2.3.6 progress_1.2.2 pillar_1.8.1
## [16] RSQLite_2.2.19 lattice_0.20-45 glue_1.6.2
## [19] digest_0.6.30 htmltools_0.5.4 Matrix_1.5-3
## [22] XML_3.99-0.13 pkgconfig_2.0.3 biomaRt_2.54.0
## [25] bookdown_0.30 zlibbioc_1.44.0 tibble_3.1.8
## [28] KEGGREST_1.38.0 generics_0.1.3 ellipsis_0.3.2
## [31] cachem_1.0.6 GenomicFeatures_1.50.3 gmapR_1.40.0
## [34] cli_3.4.1 magrittr_2.0.3 crayon_1.5.2
## [37] memoise_2.0.1 evaluate_0.18 fansi_1.0.3
## [40] xml2_1.3.3 tools_4.2.2 prettyunits_1.1.1
## [43] hms_1.1.2 BiocIO_1.8.0 lifecycle_1.0.3
## [46] stringr_1.5.0 DelayedArray_0.24.0 AnnotationDbi_1.60.0
## [49] compiler_4.2.2 jquerylib_0.1.4 rlang_1.0.6
## [52] grid_4.2.2 RCurl_1.98-1.9 rjson_0.2.21
## [55] rappdirs_0.3.3 bitops_1.0-7 rmarkdown_2.18
## [58] restfulr_0.0.15 codetools_0.2-18 curl_4.3.3
## [61] DBI_1.1.3 R6_2.5.1 GenomicAlignments_1.34.0
## [64] rtracklayer_1.58.0 knitr_1.41 dplyr_1.0.10
## [67] utf8_1.2.2 fastmap_1.1.0 bit_4.0.5
## [70] filelock_1.0.2 stringi_1.7.8 parallel_4.2.2
## [73] Rcpp_1.0.9 vctrs_0.5.1 png_0.1-8
## [76] tidyselect_1.2.0 dbplyr_2.2.1 xfun_0.35