TFtab: TF-binding score table extracted from a 'taxaTF' class

Description Usage Arguments Value

Description

Generate an TF binding score table from a taxaTF class

Usage

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TFtab(objects = NULL, taxa = "all", tf = "all", rowindex = NULL,
  filtering = TRUE, normalize = TRUE, logrithm = TRUE)

Arguments

objects

a vector of objects of class taxonTF or an object of class taxaTF

taxa

one single character or a vector of characters specifying main taxa to be included in the TF binding score table. taxa usually corresponds to species tissues or cell line types. If one single character "all" is given, all the taxa included in the taxaTF will be matched and included ("all" by default).

tf

one single character or a vector of characters specifying transcription factor(s) to be included in the TF binding score table. If one single character "all" is given, all the transcription factor included in the taxaTF will be matched and included ("all" by default).

rowindex

a vector of numbers corresponded to indices of selecting rows

filtering

a logical specifying whether to exclude genes with binding score equal to 0 in all taxaon and tfs.

normalize

a logical specifying whether to perform quantile normalization on sample-specific biases.

logrithm

a logical specifying whether to apply TF binding score log2 tranformation (TRUE by default).

Value

An TF binding score table: column corresponds to median binding score value of all biological samples within one taxa_TF group; row corresponds to othologous genes


jingwyang/AnceTran documentation built on May 19, 2019, 2:57 a.m.