append_ynorm: append_ynorm

In seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

Description

see calc_norm_factors for normalization details.

Usage

append_ynorm(
  full_dt,
  value_ = "y",
  cap_value_ = "y_cap_value",
  norm_value_ = "y_norm",
  by1 = "id",
  by2 = "sample",
  aggFUN1 = max,
  aggFUN2 = function(x) quantile(x, 0.95),
  cap_dt = NULL,
  do_not_cap = FALSE,
  force_append = FALSE
)

Arguments

full_dt	a data.table, as returned by ssvFetch*(..., return_data.table = TRUE).
value_	character, attribute in full_dt to normalzie.
cap_value_	character, new attribute name specifying values to cap to.
norm_value_	character, new attribute name specifying normalized values.
by1	character vector, specifies attributes relevant to step 1.
by2	character vector, specifies attributes relevant to step 1 and 2.
aggFUN1	function called on value_ with by = c(by1, by2) in step 1.
aggFUN2	function called on result of aggFUN1 with by = by2 in step 2.
cap_dt	optionally, provide user generated by2 to cap_value_ mapping
do_not_cap	if TRUE, normalized values are not capped to 1. Default is FALSE.
force_append	if TRUE, any previous cap_value or norm_value is overridden. Default is FALSE.

Value

data.table, full_dt with cap_value_ and norm_value_ values appended.

Examples

append_ynorm(CTCF_in_10a_profiles_dt)
append_ynorm(CTCF_in_10a_profiles_dt,
  aggFUN1 = mean, aggFUN2 = function(x)quantile(x, .5))

seqsetvis documentation built on Nov. 8, 2020, 5:57 p.m.