timecourseTable: constructs time course table for clustering analysis

In MengjunWu/TCseq: Time course sequencing data analysis

constructs time course table for clustering analysis

Description

This function constructs a time course table of which rows are genomic features and columns time points. values can be normalized expression levels or log2-fold changes compared to a control time point. The time course table is used for clustering analysis.

Usage

timecourseTable(
  object,
  value = "expression",
  control.group = NULL,
  lib.norm = TRUE,
  norm.method = "rpkm",
  subset = NULL,
  filter = FALSE,
  pvalue = "fdr",
  pvalue.threshold = 0.05,
  abs.fold = 2,
  direction = "both",
  ...
)

Arguments

object	a TCA object returned by DBanalysis.
value	a character string, either "expression" or "FC". "expression" is the mean normalized read counts of replicates, "FC" is the log2-fold changes compared to the first time point.
control.group	a character string giving the time point to be compared with, i.e., the denominator in the fold changes. It should match one of the time points in the design table in the TCA object.
lib.norm	logical indicating whether or not use effective library size (see "Details" in counts).
norm.method	a character string specifying the normalization method if value is "expression"
subset	an optinal character vector giving a subset of genomic features, if not NULL, time course table is generated for only this subset of genomic features.
filter	logical, whether to drop the genomic features shows no significant changes (defined by pvalue, pvalue.threshold,abs.fold and direction) between any two time points.
pvalue	character string specify the type of p-values: "none" is unadjusted p-value or one of adjusted p-value "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr".
pvalue.threshold	a numeric value giving threshold of selected p-value, significant changes have lower (adjusted) p-values than the threshold.
abs.fold	a numeric value, the least minimum log2-fold changes. The returned genomic regions have changes with absolute log2-fold changes exceeding abs.fold.
direction	character string specify the direction of fold changes. "up": positive fold changes; "down": negative fold changes; "both": both positive and negative fold changes.
...	additional arguments passing to rpkm, cpm

Value

A TCA object

Note

If "expression" in value is chosen, the average normalized expression values of replicates for each group will be calculated and returned.

Author(s)

Mengjun Wu

Examples

data(tca_ATAC)
tca_ATAC <- DBanalysis(tca_ATAC)
tca_ATAC <- timecourseTable(tca_ATAC, value = 'expression',
                            lib.norm = TRUE, norm.method = 'rpkm')

MengjunWu/TCseq documentation built on May 15, 2023, 9:47 p.m.