crossTab-class: An S4 class 'crossTab'

In coRdon: Codon Usage Analysis and Prediction of Gene Expressivity

Description

Contingency table of sequences' annotations and the corresponding numeric values.

Usage

crossTab(sequences, variable, threshold = 1L, percentiles = NULL)

## S4 method for signature 'character,numeric'
crossTab(sequences, variable,
  threshold = 1L, percentiles = NULL)

getSeqAnnot(x)

## S4 method for signature 'crossTab'
getSeqAnnot(x)

getVariable(x)

## S4 method for signature 'crossTab'
getVariable(x)

contable(x)

## S4 method for signature 'crossTab'
contable(x)

Arguments

sequences	Character vector of sequences' annotations (KO, COG).
variable	Numeric vector of the coresponding CU values.
threshold	A threshold value (or a vector of values) of the variable. Sequences with value of the given variable greater than threshold are taken as a subset. Default is 1. If no threshold should be set, specify threshold = NULL
percentiles	A single value or a vector of values between 0 and 1. Sequences with value of the given variable in the top percentiles are taken as a subset. If no percentiles should be specified, the argument takes the value NULL.
x	A crossTab object.

Value

Returns a crossTab object with category values in rows, and with separate columns for counts in background (all) and subsets, i.e. for diferrent thresholds/percentiles provided.

Methods (by generic)

• crossTab: Create a contingency table for the set of annotated sequences and the corresponding codon usage (CU) values.

• getSeqAnnot: Get sequence annotations from crossTab object.

• getVariable: Get values of the variable used to create contingency table in crossTab object.

• contable: Get contingency table from crossTab object.

Slots

sequences

Character vector of sequences annotations.

variable

Numeric vector of the coresponding CU values.

table

Contingecy table.

Examples

set.seed(5491)
s <- sample(LETTERS[1:3], 10, replace = TRUE)
v <- sample(1:5, 10, replace = TRUE)
crossTab(s, v)
crossTab(s, v, threshold = c(3,5))
crossTab(s, v, threshold = NULL, percentiles = c(0.5, 0.3))
ct <- crossTab(s, v)
contable(ct)
getSeqAnnot(ct)
getVariable(ct)

coRdon documentation built on Nov. 8, 2020, 5:28 p.m.