Combine GwasSumStats collections

Row-bind two or more GwasSumStats collections into one – e.g. the per-LD-block pieces a block-parallel pipeline writes, back into the single block-keyed collection assembleCtwasInputs requires. Per-element metadata (blockId, varY, nCase / ...) is carried through; a collection lacking an optional column is NA-padded.

Usage

combineGwasSumStats(..., ldSketch = NULL)

Arguments

...

Two or more GwasSumStats objects, or a single list of them.

ldSketch

Optional genotype panel (see readGenotypes) to attach to the combined collection, overriding the unioned one. Default NULL.

Value

A single combined GwasSumStats.

Details

The three collection-level slots are merged rather than taken from the first input: genome and the summaryStatsQc options must agree across the inputs (a mismatch is an error, not a silent first-wins), the per-element qcInfo$entryAudit concatenates in element order so getQcDiagnostics keeps addressing the right element, and the LD sketches union into one panel over the shared genotype handle. That last one matters: block-parallel pipelines narrow each piece's panel to its own block, so keeping only the first would leave a multi-block collection whose LD reference covers one block.

See also

combineQtlSumStats, combineFineMappingResults, combineTwasWeights

Examples

data(gwasSumStatsS4Example)
combineGwasSumStats(gwasSumStatsS4Example)
#> GwasSumStats: 1 studies, genome build hg19
#>   LD sketch: plink1 @ pecotmr://extdata/toy_canonical