Reference

All functions

FLASHFMwithJAMd()

Wrapper for flashfm Multi-Trait Fine-Mapping with JAM - this is the dynamic number of max causal variant version

JAMdynamic()

Expanded version of JAM (a single-trait fine-mapping approach) that first runs on thinned SNPs and then expands models on tag SNPs This version starts at a low upper bound for max causal variants and decides on max upper bound based on data

MGFLASHFMwithJAM()

Wrapper for Multi-group multi-trait fine-mapping, using FLASHFMwithJAM

MGFMwithJAM()

Wrapper for credible sets from Multi-Group Single-Trait Fine-Mapping with JAM

MGflashfm()

Multi-group multi-trait fine-mapping, using output from FLASHFMwithJAM or FLASHFMwithFINEMAP; gives both multi- and single-trait results from flashfm object

MGflashfmRET()

Multi-group multi-trait fine-mapping, using output from FLASHFMwithJAM or FLASHFMwithFINEMAP; gives both multi- and single-trait results from flashfm object

MGfm()

Multi-Group Single-Trait Fine-Mapping credible sets

Nall

List of samples size vectors for two simulated traits in two groups

Neff()

Approximate effective sample size from GWAS of related samples (copied from flashfm)

allcredsetsPP()

Construct a credible set for each trait and under each of single and multi-trait fine-mapping, and provide SNP PP details

corX.list

List of SNP correlation matrices for two groups

covY.list

Covariance matrices for two simulated traits in two groups

cvs

Vector of rsids for causal variants of two simulated traits in two groups

g2t1CS

Output from running JAMdynamic on Group 2, Trait 1 simulated dataset in this package

groupmultiU()

Group SNPs; adapted from group.multi by Chris Wallace

gwas.list

List of GWAS results for two traits in two groups

makeSNPgroups2U()

Make two sets of SNP groups using fine-mapping information from all of the traits using two sets of results and maps the names between them

makeSNPgroupsU()

Make SNP groups using fine-mapping information from all of the traits

mgmtCS

Output from running MGFLASHFMwithJAM on the simulated dataset in this package