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Rows of a polarity table that need a human decision

Source: R/polarity_table.R
dmsa_polarity_review.Rd

Three kinds of row should never be used without someone looking at them: a sign the curator and a database disagree about, a sign no evidence could settle, and a non-zero sign held at low confidence. This returns them.

Usage

dmsa_polarity_review(
  x = "alpha",
  which = c("all", "disagreement", "unresolved", "low_confidence")
)

Arguments

x

A dmsa_polarity, or anything dmsa_polarity() accepts - including a dmsa_selection, which scopes the review to that selection's genes.

which

"all", "disagreement" (a database contradiction or a framing choice only the analyst can settle), "unresolved" or "low_confidence".

Value

data.frame of class dmsa_polarity_review.

Examples

## The three kinds of row nobody should use unseen: a database contradiction,
## a sign no evidence settles, and a non-zero sign held at low confidence.
flagged <- dmsa_polarity_review(dmsa_select(systems = "hpa"))
table(flagged$review_flag)
#> 
#>     low_confidence_signed unresolved_needs_evidence 
#>                         7                         1 
## a disagreement is a framing call the analyst has to make, not a bug
dmsa_polarity_review(which = "disagreement")$gene
#> [1] "FOXL2"   "ADORA2A" "ADORA2B" "REST"    "PHOX2A"  "PHOX2B"  "EP300"  
#> [8] "FOXP2"   "PAX8"