CAMERA_local class — CAMERA

A simple wrapper function for importing data from local files for use with the CAMERA class.

Public fields

metadata: Data frame with information about the data. One row per dataset. See details for info on columns
ld_ref: Data frame with two columns - pop = population (referencing the pop values in metadata), bfile = path to plink file for that reference
mc.cores: The number of processor cores to use
plink_bin: Location of executable plink (version 1.90 is recommended)
minmaf: Minimum allele frequency per dataset
pthresh: P-value threshold for instrument inclusion
instrument_raw: A data frame of pooled instruments across all ancestries, that has been extracted from each ancestry for the exposure traits
instrument_outcome: Instruments in instrument_raw extracted from the outcome datasets
instrument_regions: Named list of data frames of length number of unique instruments in instrument_raw. Names of each item are the instruments. Each item is a list of regional extracts around the instrument from each population exposure study.
instrument_outcome_regions: As per instrument_regions but for the outcome datasets.

Methods

Public methods

CAMERA_local$new()
CAMERA_local$standardise()
CAMERA_local$read_file()
CAMERA_local$pool_tophits()
CAMERA_local$organise_data()
CAMERA_local$fixed_effects_meta_analysis_fast()
CAMERA_local$organise()
CAMERA_local$clone()

`CAMERA_local$new()`

Create a new dataset and initialise an R interface

Usage

CAMERA_local$new(
  metadata,
  ld_ref,
  plink_bin,
  mc.cores = 1,
  radius = 25000,
  pthresh = 5e-08,
  minmaf = 0.01
)

Arguments

metadata: Data frame with information about the data. One row per dataset. See details for info on columns
ld_ref: Data frame with two columns - pop = population (referencing the pop values in metadata), bfile = path to plink file for that reference
plink_bin: Location of executable plink (version 1.90 is recommended)
mc.cores: Number of cores to use
radius: Genomic window size to extract SNPs
radius: Default 250000
pthresh: P-value threshold for instrument inclusion
minmaf: Minimum allele frequency per dataset

`CAMERA_local$standardise()`

Standardise the allele coding

Usage

CAMERA_local$standardise(
  d,
  ea_col = "ea",
  oa_col = "oa",
  beta_col = "beta",
  eaf_col = "eaf",
  chr_col = "chr",
  pos_col = "pos",
  vid_col = "vid"
)

Arguments

d: data.frame
ea_col: Column name for effect allele
oa_col: Column name for other allele
beta_col: Column name containing beta coefficients
eaf_col: Column name containing allele frequency for effect allele
chr_col: Column name containing chromosome
pos_col: Column name containing position
vid_col: Column name containing variant ID

`CAMERA_local$read_file()`

Function to read in a file

Usage

CAMERA_local$read_file(m, minmaf = 0.01)

Arguments

m: File object
minmaf: Minimum allele frequency per dataset

`CAMERA_local$pool_tophits()`

Pool the top hits

Usage

CAMERA_local$pool_tophits(
  rawdat,
  tophits,
  metadata,
  radius = 250000,
  pthresh = 5e-08,
  mc.cores = 10
)

Arguments

rawdat: The raw data
tophits: The top hits
metadata: Data frame with information about the data. One row per dataset. See details for info on columns
radius: Genomic window size to extract SNPs
radius: Default 250000
pthresh: P-value threshold for instrument inclusion
mc.cores: Number of cores to use

`CAMERA_local$organise_data()`

A function to organise the data

Usage

CAMERA_local$organise_data(
  metadata = self$metadata,
  plink_bin = self$plink_bin,
  ld_ref = self$ld_ref,
  pthresh = self$pthresh,
  minmaf = self$minmaf,
  radius = self$radius,
  mc.cores = self$mc.cores
)

Arguments

metadata: Data frame with information about the data. One row per dataset. See details for info on columns
plink_bin: Location of executable plink (version 1.90 is recommended)
ld_ref: Data frame with two columns - pop = population (referencing the pop values in metadata), bfile = path to plink file for that reference
pthresh: P-value threshold for instrument inclusion
minmaf: Minimum allele frequency per dataset
radius: Genomic window size to extract SNPs
radius: Default 250000
mc.cores: Number of cores to use

`CAMERA_local$fixed_effects_meta_analysis_fast()`

A function to perform fixed effect meta-analysis

Usage

CAMERA_local$fixed_effects_meta_analysis_fast(beta_mat, se_mat)

Arguments

beta_mat: Matrix of beta coefficients
se_mat: Matrix of SEs

`CAMERA_local$organise()`

Organise the output

Usage

CAMERA_local$organise()

`CAMERA_local$clone()`

The objects of this class are cloneable with this method.

Usage

CAMERA_local$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.