Loading required namespace: GenomicFiles
Using local VCF.
File already tabix-indexed.
Finding empty VCF columns based on first 10,000 rows.
1 sample detected: ieu-b-116
Constructing ScanVcfParam object.
VCF contains: 64,421 variant(s) x 1 sample(s)
Processing will be more efficient in single-threaded mode when nrows<100000. Temporarily setting nThread=1.
Reading VCF file: single-threaded
Converting VCF to data.table.
Expanding VCF first, so number of rows may increase.
Checking for empty columns.
Unlisting 4 columns.
VCF data.table contains: 64,421 rows x 11 columns.
Renaming ID as SNP.
VCF file has -log10 P-values; these will be converted to unadjusted p-values in the 'P' column.
No INFO (SI) column detected.
Standardising column headers.
First line of summary statistics file: 
SNP	chr	BP	end	REF	ALT	FILTER	ES	SE	LP	SS	P	
Summary statistics report:
   - 64,421 rows
   - 64,421 unique variants
   - 73 genome-wide significant variants (P<5e-8)
   - 22 chromosomes
Checking for multi-GWAS.
Checking for multiple RSIDs on one row.
Inferring genome build.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 10,000 SNPs using BSgenome::snpsById...
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

BSgenome::snpsById done in 23 seconds.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 10,000 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 65 seconds.
Inferred genome build: GRCH37
Checking SNP RSIDs.
Checking for merged allele column.
Checking A1 is uppercase
Checking A2 is uppercase
Checking for incorrect base-pair positions
Ensuring all SNPs are on the reference genome.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 64,421 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 12 seconds.
4,263 SNPs are not on the reference genome. These will be corrected from the reference genome.
Loading SNPlocs data.
Sorting coordinates with 'data.table'.
Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-116/logs/snp_not_found_from_chr_bp.tsv
Writing uncompressed instead of gzipped to enable tabix indexing.
Converting full summary stats file to tabix format for fast querying...
Reading header.
Ensuring file is bgzipped.
Tabix-indexing file.
Removing temporary .tsv file.
Loading SNPlocs data.
Loading reference genome data.
Preprocessing RSIDs.
Validating RSIDs of 63,821 SNPs using BSgenome::snpsById...
BSgenome::snpsById done in 13 seconds.
Checking for correct direction of A1 (reference) and A2 (alternative allele).
Reordering so first three column headers are SNP, CHR and BP in this order.
Reordering so the fourth and fifth columns are A1 and A2.
Checking for missing data.
Checking for duplicate columns.
Ensuring that the N column is all integers.
The sumstats N column is not all integers, this could effect downstream analysis. These will be converted to integers.
Checking for duplicate SNPs from SNP ID.
Checking for SNPs with duplicated base-pair positions.
INFO column not available. Skipping INFO score filtering step.
Filtering SNPs, ensuring SE>0.
Ensuring all SNPs have N<5 std dev above mean.
Checking for bi-allelic SNPs.
1,660 SNPs are non-biallelic. These will be removed.
Sorting coordinates with 'data.table'.
Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-116/logs/snp_bi_allelic.tsv
Writing uncompressed instead of gzipped to enable tabix indexing.
Converting full summary stats file to tabix format for fast querying...
Reading header.
Ensuring file is bgzipped.
Tabix-indexing file.
Removing temporary .tsv file.
Computing Z-score from P using formula: `sign(BETA)*sqrt(stats::qchisq(P,1,lower=FALSE)`
N already exists within sumstats_dt.
Sorting coordinates with 'data.table'.
Sorting coordinates with 'data.table'.
Writing in tabular format ==> /rds/general/project/neurogenomics-lab/ephemeral/MAGMA_Files_Public/data/GWAS_munged/ieu-b-116/ieu-b-116.tsv
Writing uncompressed instead of gzipped to enable tabix indexing.
Converting full summary stats file to tabix format for fast querying...
Reading header.
Ensuring file is bgzipped.
Tabix-indexing file.
Removing temporary .tsv file.
Summary statistics report:
   - 62,161 rows (96.5% of original 64,421 rows)
   - 62,161 unique variants
   - 71 genome-wide significant variants (P<5e-8)
   - 22 chromosomes
Done munging in 2.418 minutes.
Successfully finished preparing sumstats file, preview:
Reading header.
          SNP CHR      BP A1 A2     END FILTER     BETA     SE       LP      N
1:  rs2905062   1  785050  G  A  785050   PASS -0.00150 0.0043 0.135448 108557
2:  rs1815606   1 1140435  G  T 1140435   PASS  0.00085 0.0025 0.136440 108557
3:  rs6603811   1 1706136  T  C 1706136   PASS -0.00450 0.0049 0.443646 108557
4:  rs7531583   1 1706160  A  G 1706160   PASS -0.00860 0.0025 3.344860 108557
5: rs12044597   1 1708801  A  G 1708801   PASS -0.00510 0.0021 1.873320 108557
              P          Z
1: 0.7320689718 -0.3423746
2: 0.7303987142  0.3445952
3: 0.3600426918 -0.9152837
4: 0.0004520016 -3.5076981
5: 0.0133868994 -2.4733073