NEWS

---

MungeSumstats 1.15.3

Bug fix

*Updated retrieval of IEU OpenGWAS to new approach requiring login. Also updated to use the IEU OpwnGWAS R package as a dependency.

MungeSumstats 1.15.2

New features

*FAQ Website updated.

MungeSumstats 1.15.1

New features

*FAQ Website added.

MungeSumstats 1.13.7

Bug fix

• infer_eff_direction now includes A0 as an ambiguous case as well as A1/A2.

New features

• eff_on_minor_alleles parameter added (off by default) - controls whether MungeSumstats should assume that the effects are majoritively measured on the minor alleles. Default is FALSE as this is an assumption that won't be appropriate in all cases. However, the benefit is that if we know the majority of SNPs have their effects based on the minor alleles, we can catch cases where the allele columns have been mislabelled.

MungeSumstats 1.13.6

New features

• Mappings added to mapping file for risk and non risk allele.

MungeSumstats 1.13.3

Bug fix

• Bug fix for check 3 in infer effect column - previously A1 & A2 were swapped when there were more matches for the ref genome in A1 rather than A2 which was incorrect. Corrected now so it will only be flipped when A2 has more matches to the reference genome.

MungeSumstats 1.13.2

New features

• Handling of -log10 p-values (outside of VCFs) added.

MungeSumstats 1.13.1

New features

• Mapping for OA (other Alllele) added to A1.

MungeSumstats 1.11.10

New features

• Can now pass local chain files for liftover (local_chain in format_sumstats() and liftover()).

MungeSumstats 1.11.9

New features

• Can now control what columns are checked for missing data (drop_na_cols in format_sumstats()). By default, SNP, effect columns and P/N columns are checked. Set to Null to check all columns or choose specific columns.

MungeSumstats 1.11.7

Bug fix

• Force no tab indexing when writing removed rows of SNPs. This avoids any issues where missing data causes sort errors.
• Issue fixed when sorting CHR column based on a format when CHR column is a factor.

MungeSumstats 1.11.6

Bug fix

• Catch for overflow when NA's in SNP col for check_no_rs_snp() check with imputation_ind=TRUE.

MungeSumstats 1.11.4

Bug fix

• Minor fix to get_genome_builds() to help with RAM & CPU usage during unit tests. No change in functionality for end user.

MungeSumstats 1.11.3

Bug fix

• For LDSC format, rename A1 and A2 as LDSC expects A1 to be the effect column rather than A2 (the opposite to MSS's default) - see more here. Although, this didn't seem to make any difference to results in tests, see more here.

MungeSumstats 1.11.2

Bug fix

• Remove unused argument make_ordered from sort_coords()
• Issue fixed with check ldsc format wehn compute_n type chosen

MungeSumstats 1.11.1

Bug fix

• Speed up unit test timing for bioc checks (predominately for linux tests)

MungeSumstats 1.9.19

New features

• infer_eff_direction parameter added so user can decide whether to run the check

Bug fix

• Typo in unit test for infer effect direction.
• IEU GWAS unit tests updated to account for server outages.

MungeSumstats 1.9.18

Bug fix

• Fixed column header mappings
  • Made all uncorrected header names uppercase and removed duplicates
  • "TOTALSAMPLESIZE" now maps to "N" instead of "NSTUDY"
  • "MAJORALLELE", "MAJOR_ALLELE", "MAJOR-ALLELE", and "MAJOR ALLELE" now map to "A1" instead of "A2"
  • Removed the mappings for "OR-A1", "OR.A1", "OR_A1", and "BETA1" because MSS assumes that A2 is the effect allele
  • Removed mappings for "A1FREQ", "A1FRQ", "AF1", "FREQ.A1.1000G.EUR", "FREQ.A1.ESP.EUR", "FREQ.ALLELE1.HAPMAPCEU", "FREQ1", "FREQ1.HAPMAP", and "FRQ_A1" because MSS defines "FRQ" to be the allele frequency of A2
  • Removed mappings for "CHR36", "BASE_GRCH36", "POSITION36", "POSGRCH36", "BASEGRCH36", "POS36", "POS GRCH36", "POS.GRCH36", "POS-GRCH36", and "POS_GRCH36" because MSS does not support the GRCh36 genome build
  • Removed the ambiguous mapping "NMISS" -> "N" because "NMISS" can refer to the number of samples with missing data
  • Removed the ambiguous mapping "WEIGHT" -> "N" because "WEIGHT" can refer to coefficient weights
• Fixed inference of allele where ambiguous (A1, A2) naming used (see infer_effect_column.R for code) but in short:
  • Three checks now made to infer which allele the effect/frequency information relates to. See infer_effect_column.R for further details.
  • See get_eff_frq_allele_combns.R for how effect/frequency columns that infer the allele are captured in the mapping file

New features

• New column header mappings:
  • "VARIANT_ID" and "RSIDS" --> "SNP"
  • "P_BOLT_LMM" --> "P"
  • "NCASES" --> "N_CAS"
  • "N_EFFECTIVE", "N_INFORMATIVE", and "TOTAL_N" --> "N"
  • "HET_P" --> "HETPVAL"
  • "HET_ISQ" --> "HETISQT"
  • "ALL_AF" --> "FRQ"
  • "DIRECT" --> "DIRECTION"
  • "ALT_EFFSIZE" --> "BETA"
  • "INFORMATIVE_ALT_AC" --> "AC"

MungeSumstats 1.9.17

Bug fix

• Cases checking ref genome where there are no indels would sometimes cause an error when joining. This resolved this issue.

MungeSumstats 1.9.16

New features

• flip_frq_as_biallelic parameter added enabling frequencies of non-bi-allelic SNPs to be flipped as if they were bi-allelic (1 - frequency) i.e. ignoring the frequencies of other alternative alleles (assuming these will be negligible). Note this will not be done as default as it is not fully correct but may be useful for some users.

MungeSumstats 1.9.15

Bug fix

• Fix for imputation column when imputing RS ID from CHR:BP. Avoids crash and ensures correct identification of imputed SNPs.
• Avoid running compute_nsize function when no imputation is wanted by user - also avoids message output in this situation.

MungeSumstats 1.9.14

Bug fix

• Fix reporting of genome-wide sign variants before formatting.

MungeSumstats 1.9.13

Bug fix

• In check_bp_range ensure that the BP column is numeric.

MungeSumstats 1.9.12

Bug fix

• In check_no_rs_snp the order of operations had to be reversed to ensure all values were present before sorting column headers when imputation_ind=TRUE and imputing rsIDs.

MungeSumstats 1.9.11

New features

• The rmv_chrPrefix parameter in format_sumstats() has been replaced with the new chr_style parameter, which allows users to specify their desired chromosome name style. The supported chromosome styles are "NCBI", "UCSC", "dbSNP", and "Ensembl" with "Ensembl" being the default.
• check_chr() now automatically removes all SNPs with nonstandard CHR entries (anything other than 1-22, X, Y, and MT in the Ensembl naming style).

MungeSumstats 1.9.10

Bug fix

• Better method to detect vcf files - looks for vcf in extension not in name.

MungeSumstats 1.9.9

Bug fix

• Check ref genome change - if not match found for either genome build, an error will now be thrown.
• Checks has been added so that if chrom col has chr as a prefix, this will be removed before testing genome build.

MungeSumstats 1.9.8

Bug fix

• Bug fix when using imputation_ind with NA in chr column.

MungeSumstats 1.9.7

New features

• ignore_multi_trait parameter added which will ignore any multi-trait p-values if set to TRUE. By default it is false to maintain the current default running conditions for MSS.

MungeSumstats 1.7.18

New features

• Check added, ensure BP is between 1 - length of chromosome using reference chromosome.

MungeSumstats 1.7.17

New features

• extra mapping for base-pair position (BP) column added

MungeSumstats 1.7.14

Bug fix

• Fix ensembl chain file retrieval so works on all environments

MungeSumstats 1.7.13

Bug fix

• write_sumstats:
  • Fix indexing issues due to incomplete genome coordinates sorting: https://github.com/neurogenomics/MungeSumstats/issues/117
  • Add default NULL to ref_genome.
  • Check ref_genome (only in conditions where its used).
• sort_coord:
  • Renamed .R file from sort_coordinates to match current function name.
  • Add multiple sort_methods, including improved/more robust data.table-native method.
  • Added dedicated unit tests within test-index_tabular.R.
• New helper function: check_numeric:
  • Ensures relevant sumstats cols are numeric.
  • Added internally to: sort_coord, read_header
• rworkflows.yml:
  • Omit Windows runner.
  • Turn on run_biocheck
• to_GRanges.R / to_VRanges.R:
  • Rename files to match current function names.
• Remove extra extdata files (I think these were created by accident):
  • ALSvcf.vcf.bgz
  • ALSvcf.vcf.bgz.bgz
  • ALSvcf.vcf.bgz.bgz.tbi
  • ALSvcf.vcf.bgz.tbi
  • ALSvcf.vcf.gz
• Remove .DS_Store files throughout.
• Don't check for duplicates based on RS ID with Indels, remove these first.

New features

• Implement rworkflows.
  • Removed old Dockerfile (not needed anymore) and workflow yaml.
• Add drop_indels parameter so a user can decide to remove indels from sumstats.

MungeSumstats 1.7.12

Bug fix

• For downloading files use sed -E rather than sed -r as its compatible with mac which has issues with sed -r

New features

• For instances where a single column contains CHR, BP, A1 and A2. The default order has been updated to CHR:BP:A1:A2 to align with
  SPDI format. If your format differs and MSS doesn't pick up on it, update the column name to the true format e.g. CHR:BP:A2:A1

MungeSumstats 1.7.11

New features

• Update to where SNP column is given by the four CHR, BP, A1, A2. Now, if A1 or A2 is also a separate column, these will be used to infer the order.

MungeSumstats 1.7.10

Bug fix

• further fix for Latex issues when rendering PDF of examples.

MungeSumstats 1.7.9

Bug fix

• fix for Latex issues when rendering PDF of examples.

MungeSumstats 1.7.3

Bug fix

• fix for offline runs and accessing chain files from 1.7.2.

MungeSumstats 1.7.2

New features

• New chain files used for lifting over the genome build from Ensembl have now been added. These will now be set as the default chain file instead of UCSC due to licensing issues. The choice to use UCSC files will still be there but the files will not be stored in the package themselves, they will instead be downloaded for use on the fly.

MungeSumstats 1.7.1

New features

• The use of the log_folder parameter in format_sumstats() has been updated. It is still used to point to the directory for the log files and the log of MungeSumstats messages to be stored. And the default is still a temporary directory. However, now the name of the log files (log messages and log outputs) are the same as the name of the file specified in the save_path parameter with the extension '_log_msg.txt' and '_log_output.txt' respectively.

MungeSumstats 1.5.18

Bug fix

• GHA fix.

MungeSumstats 1.5.17

New features

• By default ES taken as BETA new parameter added so users can specify if this isn't the case (es_is_beta). If set to FALSE, mapping removed.
• Imputing BETA ordering has been changed so log(OR) will be sued before calculating from Z, SE.

MungeSumstats 1.5.16

New features

• A new method for computing the Z-score of a sumstats (compute_z input) has been added: BETA/SE. To use it set compute_z = 'BETA' to continue to use the P-value calculation use compute_z = 'P'. Note the default is stil compute_z = FALSE.

Bug fix

• Remove erroneous print statement.

MungeSumstats 1.5.15

Bug fixes

• Fix NA representation for tabular outputs - By default, data.table::fread() leaves NAs blank instead of including a literal NA. That's fine for CSVs and if the output is read in by fread, but it breaks other tools for TSVs and is hard to read. Updated that and added a message when the table is switched to uncompressed for indexing.

MungeSumstats 1.5.14

New features

• read_header:
  • Can now read entire files by setting n=NULL.
  • Improved reading in of VCF files (can read .vcf.bgz now).
  • Now exported.
  • Added unit tests.
• Remove seqminer from all code (too buggy).
• Automatically remove residual .tsv files after tabix indexing.
• import_sumstats:
  • Use @inheritDotParams format_sumstats for better documentation.
• parse_logs: Added new fields.
• format_sumstats: Added time report at the end (minutes taken total). Since this is a message, will be included in the logs, and is now parsed by parse_logs and put into the column "time".

Bug fixes

• index_tabular: Fixed by replacing seqminer with Rsamtools.
• When SNP ID's passed with format 1:123456789, it will now be dealt with appropriately.
• compute_n can't handle SNP level N values for imputation only population level. An explanatory error message has now been added.

MungeSumstats 1.5.13

Bug fixes

• Special characters causing issues with find empty columns function. Now fixed.

MungeSumstats 1.5.12

Bug fixes

• Mitchondrial (MT) SNPs' chromosome value were being forced to NA by sort_coords function. This has been fixed.

MungeSumstats 1.5.11

Bug fixes

• Had to pass check_dups to other checks so they also wouldn't be run. Now independent of non-biallelic check.

MungeSumstats 1.5.10

New features

• check_dups parameter added so duplicates won't be removed if formatting QTL datasets

MungeSumstats 1.5.9

Bug fixes

• validate_parameters checks for incorrect version of dbSNP package, corrected.

MungeSumstats 1.5.6

Bug fixes

• MSS can now impute CHR, BP at a SNP level. For cases where CHR and/or BP are NA but the RS ID is present, these will now be imputed fromt he reference genome. Note previously, this imputation was done when the chr and/or bp column was missing.
• Print statement from liftover silenced when no liftover required
• check missing data function will no longer remove cases with NA's in SNP_INFO column. The SNP_INFO column is created by MSS for cases with RS ID and some other information in the same SNP column (like rs1234:.....). Rather than throw out this info, it is stored in a new column - SNP_INFO. However, the remove missing data function was also looking in this column to remove SNPs. This has been corrected.
• find_sumstats():
  • Fix N column in metadata.

MungeSumstats 1.5.5

New features

• save_format parameter created for format_sumstats. This will replace ldsc_format which is now deprecated. Use save_format="LDSC" instead. Other options for save_format are generic standardised (NULL) and IEU Open GWAS VCF format ("openGWAS").
• dbSNP version 155 has now been added. Users can now control the version of dbSNP to be used for imputation (144 or 155). Note that with the 9x more SNPs in dbSNP 155 vs 144, run times will increase.

Bug fixes

• Change where sex chromosomes were made lower case removed to match UCSC

MungeSumstats 1.5.4

New features

• Further mappings added

Bug fixes

• Duplication of non-bi-allelic and indels fixed
• Correct compute_nsize documentation

MungeSumstats 1.5.1

New features

• Export vcf2df.
  • Move some post-processing function inside this function (e.g. drop duplicate cols/rows).
• read_vcf can now be parallised: splits query into chunks, imports them, and (optionally) converts them to data.table before rbinding them back into one object.
  • Added report of VCF size (variants x samples) before processing to give user an idea of long it will take to process.
  • Added arg mt_thresh to avoid using parallelisation when VCFs are small, due to the overhead outweighing the benefits in these cases.
• Added Linux installation instructions for axel downloader.
• Added 2nd tryCatch to downloader with different download.file parameters that may work better on certain machines.
• Avoid using file.path to specify URL in:
  • get_chain_file
  • import_sumstats
• Allow download_vcf to pass URLs directly (without downloading the files) when vcf_download=FALSE.
• download_vcf:
  • Make timeout 10min instead of 30min.
  • Make axel verbose.
• load_ref_genome_data:
  • Give more informative messages that let user know which steps take a long time.
  • Speed up substring preprocessing.
• read_vcf_genome: more robust way to get genome build from VCF.
• read_sumstats: Speed up by using remove_empty_cols(sampled_rows=), and only run for tabular file (read_vcf already does this internally).

Bug fixes

• select_vcf_field: Got rid of "REF col doesn't exists" warning by omitting rowRanges.
• Ensured several unevaluated code chunks in vignettes/MungeSumstats.Rmd were surrounding by ticks.
• vcf2df: Accounted for scenarios where writeVcf accidentally converts geno data into redundant 3D matrices.
  • Use data.table::rbindlist(fill=TRUE) to bind chunks back together.
• Remove unused functions after read_vcf upgrades:
  • infer_vcf_sample_ids
  • is_vcf_parsed
  • check_tab_delimited
  • read_vcf_data
  • remove_nonstandard_vcf_cols
• Remove redundant dt_to_granges by merging functionality into to_granges.
  • Adjusted liftover to accommodate the slight change.
• Fix is_tabix (I had incorrectly made path all lowercase).
• Let index_vcf recognize all compressed vcf suffixes.
  • Add extra error handling when .gz is not actually bgz-compressed.
• Set BiocParallel registered threads back to 1 after read_vcf_parallel finishes, to avoid potential conflicts with downstream steps.

MungeSumstats 1.5.0

New features

• Added "query" column to find_sumstats output to keep track of search parameters.
• import_sumstats:
  • Check if formatted file (save_path) exists before downloading to save time.
  • Pass up force_new in additional to force_new_vcf.
• Updated Description tag in DESCRIPTION file to better reflect the scope of MungeSumstats.
• Upgraded read_vcf to be more robust.
• Edited Deps/Suggests
  • Elevate IRanges to Imports.
  • Remove stringr (no longer used)
• Add new internal function is_tabix to check whether a file is already tabix-indexed.
• read_sumstats:
  • now takes samples as an arg.
  • Parallises reading VCF using GenomicFiles.
• read_sumstats: now takes samples as an arg.
  By default, only uses first sample (if multiple are present in file).
• Remove INFO_filter= from ALS VCF examples in vignettes (no longer necessary now that INFO parsing has been corrected).
• download_vcf can now handle situations with vcf_url= is actually a local file (not remote).

Bug fixes

• AF (allele frequency) was accidentally being assigned as INFO column in VCFs where the INFO rows started with "AF". This caused a large number of SNPs to be incorrectly dropped during the check_info_score step.
• If INFO score is not available, INFO column is now dropped entirely (rather than assigning all 1s).
  • Adjusted test-vcf_formatting to reflect this. This avoids ambiguity about whether the INFO score is real or not.
• check_info_score:
  • Added extra messages in various conditions where INFO is not used for filtering, and don't add log_files$info_filter in these instances.
  • Added unit tests.
• check_empty_cols was accidentally dropping more columns than it should have.
• Fix GHA pkgdown building:
  • The newest version of git introduced bugs when building pkgdown sites from within Docker containers (e.g. via my Linux GHA workflow). Adjusting GHA to fix this.
• Fix write_sumstats when indexing VCF.
• Ensure read_sumstats can read in any VCF files (local/remote, indexed/non-indexed).
• Fix test-vcf_formatting.R
  • line 51: had wrong AF value in string
  • line 109: encountering error? due to duplicate SNPs?
• Fix test-check_impute_se_beta
  • lines 51/52: setkey on SNP (now automatically renamed from ID by read_vcf).
• Fix test-read_sumstats:
  • standardising of headers is now handled internally by read_sumstats.
  • Ensure CHR is a character vector when being read in.
  • line 44: Ensure extra cols in vcf_ss are dropped.
• parse_logs: Add lines to parsing subfunctions to allow handling of logs that don't contain certain info (thus avoid warnings when creating the final data.table).
• 'Avoid the use of 'paste' in condition signals' fixed:
  • check_pos_se
  • check_signed_col
• Used to rely on gunzip to read bgz files, but apparently this functionality is no longer supported (possibly due to changes to how Rsamtools::bgzip does compression in Bioc 3.15. Switched to using fread + readLines in:
  • read_header
  • read_sumstats
• read_header: wasn't reading in enough lines to get past the VCF header. Increase to readLines(n=1000).
• read_vcf: Would sometimes induce duplicate rows. Now only unique rows are used (after sample and columns filtering).
• Issue with mix of chr:bp:a1:a2 and chr:bp and rs id resolved

MungeSumstats 1.3.19

Bug fixes

• format_sumstats can now import remote files (other than OpenGWAS).

New features

• New sumstatsColHeaders entries:
  • "PosGRCh37" --> "BP"
  • "testedAllele" --> "A1"

MungeSumstats 1.3.18

New features

• Can now handle general remote sumstats not just IEU GWAS
• More column header mappings

MungeSumstats 1.3.17

New features

• Clean up of column header mapping file, including FREQUENCY given priority over MAF and addition of new CHR mappings.

MungeSumstats 1.3.15

Bug fixes

• Handle cases for multi-trait GWAS when P columns exists separate to the trait specific P value so that when renaming occurs there isn't two P columns. Inputted P column will be renamed to 'P_input'
• Issue where 'check allele flip' wasn't running when the sumstats had all SNP IDs missing and incorrect direction of A1/A2 and effect columns has now been fixed.

MungeSumstats 1.3.14

New features

• liftover
  • Now exported function.
  • Added args for more user flexibility.
  • Uses GenomeInfoDb::mapGenomeBuilds to standardise build names.
  • Warns users when mapped builds do not match one of the conversion options.
  • Choice to output as data.table or GRanges.
  • Added units tests for exported version.
• standardise_sumstats_column_headers_crossplatform
  • Exported as standardise_header while keeping the original function name as an internal function (they call the same code).
  • Added unit tests for exported version.
• Added chunks to *Getting started` vignette
  • liftover tutorial
  • "Quick formatting" of headers and file formats.

Bug fixes

• check_pos_se: Remove extra message() call around string.
• check_signed_col: Remove extra message() call around string.
• write_sumstats
  • Added extra round of sorting when tabix_index=TRUE because this is required for tabix.

MungeSumstats 1.3.13

New Features

• Additional mappings for CHR
• Make A1, A2 upper-case

Bug fixes

• Bug fix for dealing with imputing SNP ID when there are indels

MungeSumstats 1.3.11

New Features

• MungeSumstats can now handle Indels better. It will:
  • Not impute the RS ID of a SNP for an Indel
  • Not remove the Indel based on the RS ID not being present in the SNP ref dataset.
  • Not remove the Indel if it has the same base-pair location as a SNP in the sumstats.
• Can now handle vcfs with extensions .vcf.tsv, .vcf.tsv.gz and .vcf.tsv.bgz

Bug fixes

• For non-bi-allelic SNP runs, no longer remove duplicated SNPs based on their base-pair position or their RS ID.

MungeSumstats 1.3.9

New Features

• Exported functions. Added examples and unit tests:
  • compute_nsize
  • standardise_sumstats_column_headers_crossplatform
  • formatted_example
• New arguments:
  • standardise_sumstats_column_headers_crossplatform: Added arg uppercase_unmapped to to allow users to specify whether they want make the columns that could not be mapped to a standard name uppercase (default=TRUE for backcompatibility). Added arg return_list to specify whether to return a named list (default) or just the data.table.
  • formatted_example: Added args formatted to specify whether the file should have its colnames standardised. Added args sorted to specify whether the file should sort the data by coordinates. Added arg return_list to specify whether to return a named list (default) or just the data.table.
• Removed codecode.yml and _pkgdown.yml files (no longer necessary).
• Added Issues templates for Bugs and Feature requests.
• Added .datatable.aware=TRUE to .zzz as extra precaution.
• vcf2df: Documented arguments.
• Made v2 of hex sticker: inst/hex/hex.png

Bug fixes

• Regenerated the gh-pages branch after it accidentally got deleted.
• Remove temporary docs/ folder.
• Updated GitHub Actions.
• Updated Dockerfile so it doesn't run checks (this is now take care of by the GHA workflow).
• Added Windows-specific folders to .Rbuildignore.
• Made to_GRanges.R and to_VRanges.R file names lowercase to be congruent with function names.

MungeSumstats 1.3.7

Bug fixes

• Bug in checking for bad characters in RSID fixed

MungeSumstats 1.3.6

New Features

• Columns Beta and Standard Error can now be imputed. However note that this imputation is an approximation so could have an effect on downstream analysis. Use with caution.

MungeSumstats 1.3.5

Bug fixes

• Flipping of Odds Ratio corrected (1/OR rather than -1*OR)

MungeSumstats 1.3.4

Bug fixes

• Issue downloading chain file resolved

MungeSumstats 1.3.3

New Features

• More mappings added to default mapping file.

MungeSumstats 1.3.2

Bug fixes

• Previously rsids with characters added (e.g. rs1234567w) would cause an error when checking for the rsid on the reference genome. This has been fixed and the correct rsid will now be imputed from the reference genome for these cases.

MungeSumstats 1.3.1

New Features

• import_sumstats: Create individual folders for each GWAS dataset, with a respective logs subfolder to avoid overwriting log files when processing multiple GWAS.
• parse_logs: New function to convert logs from one or more munged GWAS into a data.table.
• list_sumstats: New function to recursively search for local summary stats files previously munged with MungeSumstats.
• Added new dataset inst/extdata/MungeSumstats_log_msg.txt to test logs files.
• Added unit tests for list_sumstats and parse_logs.
• Added new Docker vignette.
• Updated GHA workflows using r_workflows.
• Remove docs/ folder as the website will now be pushed to the gh-pages branch automatically by new GHA workflow.
• Made documentation in README more clear and concise.
• Added checks for p-values >1 or <0 via args convert_large_p and convert_neg_p, respectively. These are both handled by the new internal function check_range_p_val, which also reports the number of SNPs found meeting these criteria to the console/logs.
• check_small_p_val records which SNPs were imputed in a more robust way, by recording which SNPs met the criteria before making the changes (as opposed to inferred this info from which columns are 0 after making the changes). This function now only handles non-negative p-values, so that rows with negative p-values can be recorded/reported separately in the check_range_p_val step.
• check_small_p_val now reports the number of SNPs <= 5e-324 to console/logs.
• Unit tests have been added for both check_range_p_val and check_small_p_val.
• parse_logs can now extract information reported by check_range_p_val and check_small_p_val.
• New internal function logs_example provides easy access to log file stored in inst/extdata, and includes documentation on how it was created.
• Both check_range_p_val and check_small_p_val now use #' @inheritParams format_sumstats to improve consistency of documentation.

Bug fixes

• Reduced vignette sizes.
• Removed usage of suppressWarnings where possible.
• Deleted old .Rproj file and hidden folder (contained large files).
• Configured .Rproj so it doesn't store large data files.
• Fix badger issues: https://github.com/GuangchuangYu/badger/issues/34
• Prevent test-index_tabix.R from running due to errors (for now).

MungeSumstats 1.3.0

New Features

• Version bump to align with Bioconductor release 3.14.

MungeSumstats 1.1.27

Bug fixes

• validate_parameters can now handle ref_genome=NULL
• .tsv.gz no longer assigned suffix .tsv.
• Made code width <80 characters.
• Changed to_GRanges/to_GRanges functions to all-lowercase functions (for consistency with other functions).
• Set nThread=1 in data.table test functions.

New Features

• Added tests for get_genome_builds
• Added early check for making sure the directory save_path is in was actually created (as opposed to finding out at the very end of the pipeline).
• Tabix-indexing now available for tabular output data.
• read_header and read_sumstats now both work with .bgz files.

MungeSumstats 1.1.26

New Features

• Extra mappings for FRQ column, see data("sumstatsColHeaders") for details

MungeSumstats 1.1.23

New Features

• format_sumstats(FRQ_filter) added so SNPs can now be filtered by allele frequency
• Mapping file now has mappings for allele frequency (AF) to FRQ
• VCF files with AF in INFO column e.g. 'AF=...' now converted to AF column
• format_sumstats(frq_is_maf) check added to infer if FRQ column values are minor/effect allele frequencies or not. frq_is_maf allows users to rename the FRQ column as MAJOR_ALLELE_FRQ if some values appear to be major allele frequencies

MungeSumstats 1.1.19

New Features

• get_genome_builds() can now be called to quickly get the genome build without running the whole reformatting.
• format_sumstats(compute_n) now has more methods to compute the effective sample size with "ldsc", "sum", "giant" or "metal".
• format_sumstats(convert_ref_genome) now implemented which can perform liftover to GRCh38 from GRCh37 and vice-versa enabling better cohesion between different study's summary statistics.

MungeSumstats 1.1.11

Bug fixes

• check_no_rs_snp can now handle extra information after an RS ID. So if you have rs1234:A:G that will be separated into two columns.
• check_two_step_col and check_four_step_col, the two checks for when multiple columns are in one, have been updated so if not all SNPs have multiple columns or some have more than the expected number, this can now be handled.
• Extra mappings for the FRQ column have been added to the mapping file

New Features

• check_multi_rs_snp can now handle all punctuation with/without spaces. So if a row contains rs1234,rs5678 or rs1234, rs5678 or any other punctuation character other than , these can be handled.
• format_sumstats(path) can now be passed a dataframe/datatable of the summary statistics directly as well as a path to their saved location.
• Input summary statistics with A0/A1 corresponding to ref/alt can now be handled by the mappign file as well as A1/A2 corresponding to ref/alt.

MungeSumstats 1.1.2

New Features

• import_sumstats reads GWAS sum stats directly from Open GWAS. Now parallelised and reports how long each dataset took to import/format in total.
• find_sumstats searches Open GWAS for datasets.
• compute_z computes Z-score from P.
• compute_n computes N for all SNPs from user defined smaple size.
• format_sumstats(ldsc_format=TRUE) ensures sum stats can be fed directly into LDSC without any additional munging.
• read_sumstats, write_sumstas, and download_vcf functions now exported.
• format_sumstats(sort_coordinates=TRUE) sorts results by their genomic coordinates.
• format_sumstats(return_data=TRUE) returns data directly to user. Can be returned in either data.table (default), GRanges or VRanges format using format_sumstats(return_format="granges").
• format_sumstats(N_dropNA=TRUE) (default) drops rows where N is missing.
• format_sumstats(snp_ids_are_rs_ids=TRUE) (default) Should the SNP IDs inputted be inferred as RS IDs or some arbitrary ID.
• format_sumstats(write_vcf=TRUE) writes a tabix-indexed VCF file instead of tabular format.
• format_sumstats(save_path=...) lets users decide where their results are saved and what they're named.
• When the save_path indicates it's in tempdir(), message warns users that these files will be deleted when R session ends.
• Summary of data is given at the beginning and the end of format_sumstats via report_summary().
• Readability of preview_sumstats() messages improved.
• New checks standard error (SE) must >0 and BETA (and other effect columns) must not equal 0: format_sumstats(pos_se=TRUE,effect_columns_nonzero=TRUE)
• Log directory containing all removed SNPs is now available and can be changed to a different directory by setting: format_sumstats(log_folder_ind=TRUE,log_folder=tempdir())
• All imputed data can now be identified with a column in the output using: format_sumstats(imputation_ind=TRUE)
• Users can now input their own mapping file to be used for the column header mapping in place of data(sumstatsColHeaders). See format_sumstats(mapping_file = mapping_file).

Bug fixes

• CHR column now standardised (X and Y caps, no "chr" prefix).
• Allele flipping done on a per-SNP basis (instead of whole-column).
• Allele flipping now includes FRQ column as well as effect columns.
• The effect allele is now interpreted as the A2 allele consistent with IEU GWAS VCF approach. A1 will always be the reference allele.
• read_vcf upgraded to account for more VCF formats.
• check_n_num now accounts for situations where N is a character vector and converts to numeric.

MungeSumstats 1.1.1

Bug fixes

• Preprint publication citation added.

MungeSumstats 1.0.0

New Features

• MungeSumstats released to Bioconductor.