Convert IPA list to a gene hit list or matrix

Convert IPA list to a gene hit list or matrix

Usage

IPAlist_to_hits(
  IPAlist,
  signColname = c("Expr Fold Change", "fold.*change", "log.*ratio", "log.*fold",
    "log.*fc", "lfc", "ratio", "fold", "fc"),
  signThreshold = 0,
  geneColname = c("name", "symbol", "ID"),
  emptyValue = 0,
  returnType = c("list", "matrix"),
  verbose = FALSE,
  ...
)

Arguments

IPAlist

list of output from importIPAenrichment()

signColname

character vector of patterns to match the colname in the 'Analysis Ready Molecules' IPA xref table which should indicate the direction of change where present.

signThreshold

numeric minimum absolute threshold, default 0, for a value in 'signColname' to be considered a non-zero change.

geneColname

character vector of patterns to match the colname in the 'Analysis Ready Molecules' IPA xref table which should indicate the gene involved. This column is validated by matching with the 'Canonical Pathways' geneID or geneNames column to ensure all values involved in pathway enrichment are also present in the xref column.

emptyValue

numeric default 0, passed to list2imSigned() to use when returnType="matrix" in the matrix for non-hits.

returnType

character string

• 'list' (default): returns a signed gene list, with integer vectors named by gene.

• 'matrix': returns a numeric matrix with gene rownames.

...

additional arguments are passed to internal functions

Value

list by default, or matrix with returnType="matrix".

Details

Given a list of IPA data produced by importIPAenrichment() produce a single list or incidence matrix representing all gene hits tested by IPA.

See also

Other jam import functions: enrichDF2enrichResult(), importIPAenrichment()