Files in neurogenomics/MungeSumstats

Standardise summary statistics from GWAS

.BBSoptions

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/rworkflows.yml

.gitignore

DESCRIPTION

NAMESPACE

NEWS.md R/DF_to_dt.R R/add_col.R R/axel.R R/check_allele_flip.R R/check_allele_merge.R R/check_bi_allelic.R R/check_bp_range.R R/check_chr.R R/check_col_order.R R/check_drop_indels.R R/check_dup_bp.R R/check_dup_col.R R/check_dup_row.R R/check_dup_snp.R R/check_effect_columns_nonzero.R R/check_empty_cols.R R/check_four_step_col.R R/check_frq.R R/check_frq_maf.R R/check_info_score.R R/check_info_score_log.R R/check_ldsc_format.R R/check_miss_data.R R/check_multi_gwas.R R/check_multi_rs_snp.R R/check_n_int.R R/check_n_num.R R/check_no_allele.R R/check_no_chr_bp.R R/check_no_rs_snp.R R/check_no_snp.R R/check_numeric.R R/check_on_ref_genome.R R/check_pos_se.R R/check_range_pval.R R/check_row_snp.R R/check_save_path.R R/check_signed_col.R R/check_small_p_val.R R/check_strand_ambiguous.R R/check_tabular.R R/check_two_step_col.R R/check_vcf.R R/check_vital_col.R R/check_zscore.R R/column_dictionary.R R/compute_nsize.R R/compute_sample_size.R R/compute_sample_size_n.R R/compute_sample_size_neff.R R/convert_sumstats.R R/data.R R/download_vcf.R R/downloader.R R/drop_duplicate_cols.R R/drop_duplicate_rows.R R/find_sumstats.R R/format_sumstats.R R/formatted_example.R R/get_chain_file.R R/get_eff_frq_allele_combns.R R/get_genome_build.R R/get_genome_builds.R R/get_unique_name_log_file.R R/get_vcf_sample_ids.R R/granges_style.R R/granges_to_dt.R R/ieugwasr.R R/import_sumstats.R R/index_tabular.R R/index_vcf.R R/infer_effect_column.R R/is_tabix.R R/liftover.R R/list_sumstats.R R/load_ref_genome_data.R R/load_snp_loc_data.R R/logs_example.R R/make_allele_upper.R R/message_parallel.R R/messager.R R/parse_dropped_INFO.R R/parse_dropped_chrom.R R/parse_dropped_duplicates.R R/parse_dropped_nonA1A2.R R/parse_dropped_nonBiallelic.R R/parse_dropped_nonRef.R R/parse_flipped.R R/parse_genome_build.R R/parse_idStandard.R R/parse_logs.R R/parse_pval_large.R R/parse_pval_neg.R R/parse_pval_small.R R/parse_report.R R/parse_snps_freq_05.R R/parse_snps_not_formatted.R R/parse_time.R R/preview_sumstats.R R/read_header.R R/read_sumstats.R R/read_vcf.R R/read_vcf_genome.R R/read_vcf_info.R R/read_vcf_markername.R R/read_vcf_parallel.R R/read_vcf_pval.R R/register_cores.R R/remove_empty_cols.R R/report_summary.R R/select_vcf_fields.R R/sort_coord_genomicranges.R R/sort_coords.R R/sort_coords_datatable.R R/standardise_sumstats_column_headers_crossplatform.R R/supported_suffixes.R

R/sysdata.rda

R/to_GRanges.R R/to_VRanges.R R/unlist_dt.R R/validate_parameters.R R/vcf2df.R R/write_sumstats.R R/zzz.R README.Rmd README.md

data/.gitignore

data/sumstatsColHeaders.rda

inst/extdata/ALSvcf.vcf

inst/extdata/ALSvcf.vcf.gz

inst/extdata/GRCh37_to_GRCh38.chain.gz

inst/extdata/GRCh38_to_GRCh37.chain.gz

inst/extdata/MungeSumstats_log_msg.txt

inst/extdata/eduAttainOkbay.txt

inst/extdata/ieu-a-298.tsv.gz

inst/hex/6MGSw0KSM8oqk8c6AsK8WocW2.jpg

inst/hex/hex.png

inst/hex/hexSticker.Rmd longtests/testthat.R longtests/testthat/test-IEU_GWAS.R longtests/testthat/test-a0_a1.R longtests/testthat/test-allele_flip.R longtests/testthat/test-bi_alllelic.R longtests/testthat/test-check_drop_indels.R longtests/testthat/test-check_imputation_cols.R longtests/testthat/test-check_impute_se_beta.R longtests/testthat/test-check_info_score.R longtests/testthat/test-check_range_pval.R longtests/testthat/test-check_small_p_val.R longtests/testthat/test-check_tabular.R longtests/testthat/test-check_vcf.R longtests/testthat/test-check_zscore.R longtests/testthat/test-combined_CHR_BP_A2_A1.R longtests/testthat/test-combined_CHR_BP_A2_A1_2.R longtests/testthat/test-combined_allele_columns.R longtests/testthat/test-combined_chr_bp.R longtests/testthat/test-combined_chr_bp_2.R longtests/testthat/test-comma_delim.R longtests/testthat/test-compute_nsize.R longtests/testthat/test-correct_format.R longtests/testthat/test-dup_col.R longtests/testthat/test-dup_rows.R longtests/testthat/test-effect_columns_nonzero.R longtests/testthat/test-frq_filter.R longtests/testthat/test-get_genome_builds.R longtests/testthat/test-headers_correct.R longtests/testthat/test-indels.R longtests/testthat/test-index_tabular.R longtests/testthat/test-infer_effect_column.R longtests/testthat/test-info_filter.R longtests/testthat/test-input_R_obj.R longtests/testthat/test-liftover.R longtests/testthat/test-list_sumstats.R longtests/testthat/test-missing_data.R longtests/testthat/test-multi_rs_snp_one_row.R longtests/testthat/test-multi_traits.R longtests/testthat/test-n_not_integer.R longtests/testthat/test-n_num.R longtests/testthat/test-no_A1_A2.R longtests/testthat/test-no_chr.R longtests/testthat/test-no_chr_bp.R longtests/testthat/test-no_rs_id.R longtests/testthat/test-no_rs_snp.R longtests/testthat/test-no_snp.R longtests/testthat/test-on_ref_genome.R longtests/testthat/test-on_x_y_mt_chr.R longtests/testthat/test-read_header.R longtests/testthat/test-read_sumstats.R longtests/testthat/test-read_vcf.R longtests/testthat/test-rs_plus.R longtests/testthat/test-signed_cols.R longtests/testthat/test-small_p_val.R longtests/testthat/test-space_delim.R longtests/testthat/test-standard_error_positive.R longtests/testthat/test-standardise_sumstats_column_headers_crossplatform.R longtests/testthat/test-strand_ambig.R longtests/testthat/test-user_mapping_file.R longtests/testthat/test-validate_parameters.R longtests/testthat/test-vcf_formatting.R longtests/testthat/test-vital_cols.R longtests/testthat/test-write_sumstats.R longtests/testthat/test-zzz.R man/DF_to_dt.Rd man/api_query.Rd man/axel.Rd man/check_access_token.Rd man/check_allele_flip.Rd man/check_allele_merge.Rd man/check_bi_allelic.Rd man/check_bp_range.Rd man/check_chr.Rd man/check_col_order.Rd man/check_drop_indels.Rd man/check_dup_bp.Rd man/check_dup_col.Rd man/check_dup_row.Rd man/check_dup_snp.Rd man/check_effect_columns_nonzero.Rd man/check_empty_cols.Rd man/check_four_step_col.Rd man/check_frq.Rd man/check_frq_maf.Rd man/check_info_score.Rd man/check_ldsc_format.Rd man/check_miss_data.Rd man/check_multi_gwas.Rd man/check_multi_rs_snp.Rd man/check_n_int.Rd man/check_n_num.Rd man/check_no_allele.Rd man/check_no_chr_bp.Rd man/check_no_rs_snp.Rd man/check_no_snp.Rd man/check_numeric.Rd man/check_on_ref_genome.Rd man/check_pos_se.Rd man/check_range_p_val.Rd man/check_row_snp.Rd man/check_save_path.Rd man/check_signed_col.Rd man/check_small_p_val.Rd man/check_strand_ambiguous.Rd man/check_tabular.Rd man/check_two_step_col.Rd man/check_vcf.Rd man/check_vital_col.Rd man/check_zscore.Rd man/column_dictionary.Rd man/compute_nsize.Rd man/compute_sample_size.Rd man/compute_sample_size_n.Rd man/compute_sample_size_neff.Rd man/convert_sumstats.Rd man/download_vcf.Rd man/downloader.Rd man/drop_duplicate_cols.Rd man/drop_duplicate_rows.Rd man/find_sumstats.Rd man/format_sumstats.Rd man/formatted_example.Rd man/get_access_token.Rd man/get_chain_file.Rd man/get_eff_frq_allele_combns.Rd man/get_genome_build.Rd man/get_genome_builds.Rd man/get_query_content.Rd man/get_unique_name_log_file.Rd man/get_vcf_sample_ids.Rd man/granges_to_dt.Rd man/gwasinfo.Rd man/hg19ToHg38.Rd man/hg38ToHg19.Rd man/ieu-a-298.Rd man/import_sumstats.Rd man/index_tabular.Rd man/index_vcf.Rd man/infer_effect_column.Rd man/is_tabix.Rd man/legacy_ids.Rd man/liftover.Rd man/list_sumstats.Rd man/load_ref_genome_data.Rd man/load_snp_loc_data.Rd man/logs_example.Rd man/make_allele_upper.Rd man/message_parallel.Rd man/messager.Rd man/parse_dropped_INFO.Rd man/parse_dropped_chrom.Rd man/parse_dropped_duplicates.Rd man/parse_dropped_nonA1A2.Rd man/parse_dropped_nonBiallelic.Rd man/parse_dropped_nonRef.Rd man/parse_flipped.Rd man/parse_genome_build.Rd man/parse_idStandard.Rd man/parse_logs.Rd man/parse_pval_large.Rd man/parse_pval_neg.Rd man/parse_pval_small.Rd man/parse_report.Rd man/parse_snps_freq_05.Rd man/parse_snps_not_formatted.Rd man/parse_time.Rd man/preview_sumstats.Rd man/raw_ALSvcf.Rd man/raw_eduAttainOkbay.Rd man/read_header.Rd man/read_sumstats.Rd man/read_vcf.Rd man/read_vcf_genome.Rd man/read_vcf_info.Rd man/read_vcf_markername.Rd man/read_vcf_parallel.Rd man/read_vcf_pval.Rd man/register_cores.Rd man/remove_empty_cols.Rd man/report_summary.Rd man/select_api.Rd man/select_vcf_fields.Rd man/sort_coord_genomicranges.Rd man/sort_coords.Rd man/sort_coords_datatable.Rd man/standardise_header.Rd man/sumstatsColHeaders.Rd man/supported_suffixes.Rd man/to_granges.Rd man/to_vranges.Rd man/unlist_dt.Rd man/validate_parameters.Rd man/vcf2df.Rd man/write_sumstats.Rd tests/testthat.R tests/testthat/test-a0_a1.R tests/testthat/test-allele_flip.R tests/testthat/test-bi_alllelic.R tests/testthat/test-check_drop_indels.R tests/testthat/test-check_impute_se_beta.R tests/testthat/test-check_info_score.R tests/testthat/test-check_range_pval.R tests/testthat/test-check_small_p_val.R tests/testthat/test-check_tabular.R tests/testthat/test-check_vcf.R tests/testthat/test-check_zscore.R tests/testthat/test-combined_CHR_BP_A2_A1.R tests/testthat/test-combined_CHR_BP_A2_A1_2.R tests/testthat/test-combined_allele_columns.R tests/testthat/test-combined_chr_bp.R tests/testthat/test-combined_chr_bp_2.R tests/testthat/test-comma_delim.R tests/testthat/test-compute_nsize.R tests/testthat/test-correct_format.R tests/testthat/test-dup_col.R tests/testthat/test-dup_rows.R tests/testthat/test-effect_columns_nonzero.R tests/testthat/test-frq_filter.R tests/testthat/test-get_genome_builds.R tests/testthat/test-headers_correct.R tests/testthat/test-indels.R tests/testthat/test-index_tabular.R tests/testthat/test-info_filter.R tests/testthat/test-input_R_obj.R tests/testthat/test-list_sumstats.R tests/testthat/test-missing_data.R tests/testthat/test-multi_rs_snp_one_row.R tests/testthat/test-multi_traits.R tests/testthat/test-n_not_integer.R tests/testthat/test-n_num.R tests/testthat/test-no_chr.R tests/testthat/test-no_chr_bp.R tests/testthat/test-no_rs_id.R tests/testthat/test-no_rs_snp.R tests/testthat/test-no_snp.R tests/testthat/test-on_x_y_mt_chr.R tests/testthat/test-read_header.R tests/testthat/test-read_sumstats.R tests/testthat/test-read_vcf.R tests/testthat/test-rs_plus.R tests/testthat/test-signed_cols.R tests/testthat/test-small_p_val.R tests/testthat/test-space_delim.R tests/testthat/test-standard_error_positive.R tests/testthat/test-standardise_sumstats_column_headers_crossplatform.R tests/testthat/test-strand_ambig.R tests/testthat/test-user_mapping_file.R tests/testthat/test-validate_parameters.R tests/testthat/test-vital_cols.R tests/testthat/test-write_sumstats.R tests/testthat/test-zzz.R

vignettes/.gitignore

vignettes/MungeSumstats.Rmd

vignettes/MungeSumstats.bib

vignettes/OpenGWAS.Rmd vignettes/docker.Rmd

vignettes/nature.csl

neurogenomics/MungeSumstats documentation built on May 2, 2024, 9:04 a.m.