aggregate_signals: aggregate_signals

In jrboyd/seqtsne: Application of t-sne to NGS Genomic Signal Profiles

aggregate_signals

Description

aggregate_signals is retrieves a single representative value for a genomic region per sample by default this is the maximum anywhere in the region but this can be overriden using xmin/xmax and agg_FUN

Usage

aggregate_signals(
  profile_dt,
  agg_FUN = max,
  y_ = "y",
  yout_ = "ynorm",
  xmin = -Inf,
  xmax = Inf,
  by_ = c("tall_var", "wide_var")
)

Arguments

profile_dt	Tidy data.table of profile information. As returned by seqsetvis::ssvFetchBam.
agg_FUN	A function appled to all y_ values in xmin to xmax range. Must accept single numeric vector and return 1 value.
y_	Variable name containing profile scores.
yout_	Variable name in output containing aggregate profile score information.
xmin	The min range of x-values to apply agg_FUN to
xmax	The max range of x-values to apply agg_FUN to
by_	Character vector of variable names to apply agg_FUN by.

Value

A data.table summarizing every profile with a single value. Suitable for input to chiptsne:::plot_binned_aggregates.

Examples

aggregate_signals(profile_dt)
aggregate_signals(profile_dt, xmin = -.2, xmax = .2, agg_FUN = mean)

jrboyd/seqtsne documentation built on Nov. 5, 2022, 6:37 a.m.