dot-calculateGCweight: Get background sequence weights for GC bins

In fmicompbio/monaLisa: Binned Motif Enrichment Analysis and Visualization

Get background sequence weights for GC bins

Description

The logic is based on Homer (version 4.11). All sequences binned depending on GC content (GCbreaks). The numbers of foreground and background sequences in each bin are counted, and weights for background sequences in bin i are defined as: weight_i = (number_fg_seqs_i / number_bg_seqs_i) * (number_bg_seqs_total / number_fg_seqs_total)

Usage

.calculateGCweight(
  df,
  GCbreaks = c(0.2, 0.25, 0.3, 0.35, 0.4, 0.45, 0.5, 0.6, 0.7, 0.8),
  verbose = FALSE
)

Arguments

df	a DataFrame with sequence information.
GCbreaks	The breaks between GC bins. The default value is based on the hard-coded bins used in Homer.
verbose	A logical scalar. If TRUE, report on GC weight calculation.

Value

a DataFrame of the same dimensions as the input df, with the columns GCfrac, GCbin and GCwgt filled in with the sequence GC content, assigned GC bins and weights to correct differences in GC distributions between foreground and background sequences.

fmicompbio/monaLisa documentation built on Nov. 2, 2024, 1:33 p.m.