Make table of fine-mapping results output for latent factors and observed traits (wrapper for FMsummary_table)

Make table of fine-mapping results output for latent factors and observed traits (wrapper for FMsummary_table)

FMsummary_table_general(
  FM_obs,
  FM_latent,
  fm_traits_obs,
  fm_traits_latent,
  cred = 0.99,
  regions = NULL,
  array_index = NULL
)

Arguments

FM_obs

observed trait fine-mapping object output from "multiJAMd"

FM_latent

latent factor object output from "flashfm" (flashfmZero or flashfm related wrappers, like "FLASHFMZEROwithJAMd") or "JAMdwithGroups"

fm_traits_obs

vector of observed trait names (same length as number of traits that were fine-mapped) and in same order as fine-mapped traits

fm_traits_latent

vector of latent factor names (same length as number of factors that were fine-mapped) and in same order as fine-mapped factors

cred

level used for credible set construction; default is 0.99

regions

data.frame with region details, where the columns are in order: "chromosom"e, "start"", "end"

array_index

row number of regions data.frame

Value

Table where each row corresponds to one trait, listing credible set size, details of variant with maximum MPP, variants with MPP>0.90 and snp groups coinciding with the variant(s)

Author

Jenn Asimit