Flag the entities to query

Sets included_in_query from the statistical cutoffs. Only these rows are sent to the backend by get_network(). Rows that fail are kept, so that get_network() can still recognize them as being in the input when a backend returns them. Rows with a missing adj.pvalue are not selected.

Usage

select_entities(
  entities,
  pvalue_cutoff = NULL,
  logfc_cutoff = NULL,
  direction = c("both", "up", "down"),
  include_infinite_fc = FALSE,
  force_include = NULL
)

Arguments

entities

entity table from prepare_entities()

pvalue_cutoff

keep rows with adj.pvalue below this. NULL applies no cutoff.

logfc_cutoff

keep rows with abs(logFC) above this, on the log scale of the input. NULL applies no cutoff.

direction

"both", "up" (logFC > 0), or "down" (logFC < 0).

include_infinite_fc

whether rows with infinite logFC (detected in one condition only) are selected regardless of pvalue_cutoff and logfc_cutoff. direction still applies.

force_include

values of id, or "namespace:identifier" groundings (e.g. "HGNC:1234"), selected regardless of the cutoffs. Entities outside the table are added with get_network(include_entities = ) instead.

Value

entities with included_in_query set, and user_added (TRUE for rows selected only through force_include).

Examples

input <- data.table::fread(system.file(
    "extdata/groupComparisonModel.csv",
    package = "MSstatsBioNet"
))
entities <- prepare_entities(input, entity_type = "protein",
                             id_type = "uniprot")
entities <- select_entities(entities, pvalue_cutoff = 0.01,
                            direction = "up")
table(entities$included_in_query)
#> 
#> FALSE  TRUE 
#>     7     3