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Check for overlapping genes between specificity scores and trait gene summaries from MAGMA.

Source: R/magma_file_helpers.R
check_overlap.Rd

Check for overlapping genes between specificity scores and trait gene summaries from MAGMA.

Usage

check_overlap(
  sscore,
  magma,
  magma_gene_col,
  warn_thresh = 0.8,
  min_intersect = 1
)

Arguments

sscore

A dgeMatrix of seismic specificity scores where each column is a cell type and row names are gene identifiers. (Note: the identifiers used should match those used in the MAGMA input)

magma

A data.frame or file path to MAGMA output for a particular GWAS with at least 2 columns: gene identifiers and z-scores.

magma_gene_col

A character string corresponding to the column name in the MAGMA data containing gene identifiers. Defaults to 'GENE' from the MAGMA output.

warn_thresh

A floating point number corresponding to the minimum percentage of overlapping genes before the warning error is displayed. Defaults to 80% overlap.

min_intersect

A floating point number representing the minimum number of overlapping genes needed for further execution. Defaults to 1.