Package: MungeSumstats 1.15.2

Alan Murphy

MungeSumstats: Standardise summary statistics from GWAS

The *MungeSumstats* package is designed to facilitate the standardisation of GWAS summary statistics. It reformats inputted summary statisitics to include SNP, CHR, BP and can look up these values if any are missing. It also pefrorms dozens of QC and filtering steps to ensure high data quality and minimise inter-study differences.

Authors:Alan Murphy [aut, cre], Brian Schilder [aut, ctb], Nathan Skene [aut]

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MungeSumstats.pdf |MungeSumstats.html✨
MungeSumstats/json (API)
NEWS

# Install 'MungeSumstats' in R:

install.packages('MungeSumstats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/neurogenomics/mungesumstats/issues

Datasets:

sumstatsColHeaders - Summary Statistics Column Headers

On BioConductor:MungeSumstats-1.15.0(bioc 3.21)MungeSumstats-1.14.1(bioc 3.20)

snp wholegenome genetics comparativegenomics genomewideassociation genomicvariation preprocessing

5.85 score 87 scripts 1.5k downloads 19 exports 91 dependencies

Last updated 22 days agofrom:12077de3ba. Checks:ERROR: 1 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 08 2024
R-4.5-win	WARNING	Nov 08 2024
R-4.4-win	WARNING	Nov 08 2024
R-4.4-mac	WARNING	Nov 08 2024
R-4.3-win	WARNING	Nov 08 2024
R-4.3-mac	WARNING	Nov 08 2024

Exports:compute_nsize download_vcf find_sumstats format_sumstats formatted_example get_genome_builds import_sumstats index_tabular infer_effect_column liftover list_sumstats load_snp_loc_data parse_logs read_header read_sumstats read_vcf standardise_header vcf2df write_sumstats

Dependencies:abind AnnotationDbi askpass assertthat BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl data.table DBI DelayedArray digest dplyr fansi fastmap formatR fs futile.logger futile.options gargle generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges glue googleAuthR httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig plogr png R.methodsS3 R.oo R.utils R6 rappdirs RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect UCSC.utils utf8 VariantAnnotation vctrs withr XML XVector yaml zlibbioc

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Ensures that parameters are compatible with LDSC format	check_ldsc_format
Check for N column if not present and user wants, impute N based on user's sample size. NOTE this will be the same value for each SNP which is not necessarily correct and may cause issues down the line. N can also be inputted with "ldsc", "sum", "giant" or "metal" by passing one or multiple of these.	compute_nsize
Download VCF file and its index file from Open GWAS	download_vcf
Search Open GWAS for datasets matching criteria	find_sumstats
Check that summary statistics from GWAS are in a homogeneous format	format_sumstats
Formatted example	formatted_example
Get combinations of uncorrected allele and effect (and frq) columns	get_eff_frq_allele_combns
Infer genome builds	get_genome_builds
UCSC Chain file hg19 to hg38	hg19ToHg38
UCSC Chain file hg38 to hg19	hg38ToHg19
Local ieu-a-298 file from IEU Open GWAS	ieu-a-298
Import full genome-wide GWAS summary statistics from Open GWAS	import_sumstats
Tabix-index file: table	index_tabular
Infer if effect relates to a1 or A2 if ambiguously named	infer_effect_column
Genome build liftover	liftover
List munged summary statistics	list_sumstats
Load the reference genome data for SNPs of interest	load_ref_genome_data
Loads the SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. Reference genome version is dependent on user input.	load_snp_loc_data
Parse data from log files	parse_logs
GWAS Amyotrophic lateral sclerosis ieu open GWAS project - Subset	raw_ALSvcf
GWAS Educational Attainment Okbay 2016 - Subset	raw_eduAttainOkbay
Read in file header	read_header
Determine summary statistics file type and read them into memory	read_sumstats
Read in VCF file	read_vcf
Register cores	register_cores
Standardise the column headers in the Summary Statistics files	standardise_header
Summary Statistics Column Headers	sumstatsColHeaders
VCF to DF	vcf2df
Write sum stats file to disk	write_sumstats