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b/man/shaPRS_blend_overlap.Rd |
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% Generated by roxygen2: do not edit by hand |
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% Please edit documentation in R/shaPRS.R |
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\name{shaPRS_blend_overlap} |
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\alias{shaPRS_blend_overlap} |
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\title{Blended shaPRS (with overlapping datasets): produce summary statistics according to a continuous weighting scheme} |
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\usage{ |
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shaPRS_blend_overlap( |
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proximal, |
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adjunct, |
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blendingFactors, |
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rho = 0, |
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discardAmbiguousSNPs = T |
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) |
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} |
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\arguments{ |
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\item{proximal}{Proximal LDPred formatted GWAS summary statistics table that has header with the following columns: chr pos SNP A1 A2 Freq1.Hapmap b se p N} |
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\item{adjunct}{dataframe for adjunct dataset of the same signature} |
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\item{blendingFactors}{a 3 column table of: SNP lFDR Qval, (produced by shaPRS_adjust)} |
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\item{rho}{(optional) sample overlap between studies} |
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\item{discardAmbiguousSNPs}{(optional) if ambiguous SNPs (G/C and A/T) should be discarded (default TRUE)} |
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} |
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\value{ |
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returns an LDPred formatted summary statistics table |
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} |
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\description{ |
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This function continuously blends the two sub-phenotype statistics |
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and generates an LDPred formatted table. |
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} |
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\examples{ |
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proximalLoc <- system.file("extdata", "phenoA_sumstats", package = "shaPRS") |
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adjunctLoc <- system.file("extdata", "phenoB_sumstats", package = "shaPRS") |
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blendFactorLoc <- system.file("extdata", "myOutput_SNP_lFDR", package = "shaPRS") |
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proximal= read.table(proximalLoc, header = TRUE) |
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adjunct= read.table(adjunctLoc, header = TRUE) |
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blendingFactors= read.table(blendFactorLoc, header = TRUE) |
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blendedSumstats = shaPRS_blend_overlap(proximal, adjunct, blendingFactors) |
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} |