produce a manhattan plot for a given study, based on specific coordinates or gene symbol with radius for flanking region

produce a manhattan plot for a given study, based on specific coordinates or gene symbol with radius for flanking region

manhattanPlot(
  studyID = "ubm-a-524",
  symbol = "BCAN",
  start = NULL,
  stop = NULL,
  chromosome = NULL,
  radius = 0,
  datasource = gwidf_2021_01_30
)

Arguments

studyID

character(1) id of study in ieugwasr::gwasinfo() catalog, defaults to "ubm-a-524", which is a study described in Elliott et al Nature October 2018

symbol

a gene symbol (to be used with genesym_to_string, implicitly); if absent, chromosome, start and end must be supplied, defaults to 'BCAN'

start

chromosomal address to start region (will have radius subtracted if supplied)

stop

chromosomal address to end region (will have radius added if supplied)

chromosome

name of chromosome in Ensembl nomenclature (e.g., 1, 2, ...)

radius

numeric default to zero, specifies flanking region

datasource

data.frame that includes study identifier id and trait for labeling

Note

Includes text component of aes() so that ggplotly can be used for hovering over SNP to reveal rsid.

Examples

# ubm-a-524 is a study of an image-derived phenotype in UK Biobank,
# specifically 'dMRI TBSS ICVF Superior longitudinal fasciculus'
# see https://dx.doi.org/10.1038%2Fs41586-018-0571-7
manhattanPlot(studyID = "ubm-a-524", symbol = "BCAN", radius=500000)
#> # A tibble: 6 × 12
#>   chr       p    beta posit…¹     n     se id    rsid  ea    nea       eaf trait
#>   <chr> <dbl>   <dbl>   <int> <dbl>  <dbl> <chr> <chr> <chr> <chr>   <dbl> <chr>
#> 1 1     0.794  0.0041  1.56e8  7916 0.0165 ubm-… rs11… T     G     0.654   IDP …
#> 2 1     0.692  0.0199  1.56e8  7916 0.0508 ubm-… rs12… A     G     0.0244  IDP …
#> 3 1     0.692  0.0078  1.56e8  7916 0.0197 ubm-… rs72… T     C     0.199   IDP …
#> 4 1     0.447  0.0125  1.56e8  7916 0.0163 ubm-… rs72… T     G     0.350   IDP …
#> 5 1     0.501 -0.081   1.56e8  7916 0.120  ubm-… rs57… A     G     0.00500 IDP …
#> 6 1     0.302  0.0167  1.56e8  7916 0.0161 ubm-… rs46… T     C     0.362   IDP …
#> # … with abbreviated variable name ¹​position