Transform deep_mutational scanning scores onto a standard scale

Source: R/standardise.R

Transform deep mutational scanning fitness scores onto a standard scale aligned to the log2 enrichment ratio (ER) scale. This scale has neutral variants at 0, deleterious variants with negative scores and beneficial variants with positive scores. Standard transforms are provided and common transforms can be passed for more unusual ones.

transform_er(x, trans = c("log2", "vamp-seq", "invert"))

Arguments

x

Vector of fitness scores
trans

Transform to apply (see description). Accepts either a string or a function.

Value

Numeric vector of transformed scores

Details

The supported transforms are:

  • log2: log2 transform to change raw read ratios onto the log2 ER scale.

  • vamp-seq: Transform scores produced by the VAMP-Seq method. These have the median null mutation at 0, neutral variants at 1 and positive variants greater than 1.

  • invert: Multiply scores by -1, for example if the experimental fitness is inverted compared to natural fitness