Type: Package
Title: Finding Rhythms Using Extended Circadian Harmonic Oscillators (ECHO)
Version: 4.0.1
Description: Provides a function (echo_find()) designed to find rhythms from data using extended harmonic oscillators. For more information, see H. De los Santos et al. (2020) <doi:10.1093/bioinformatics/btz617> .
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: minpack.lm (≥ 1.2.1), boot (≥ 1.3-22)
URL: https://github.com/delosh653/ECHO
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2020-06-10 13:45:25 UTC; delosh
Author: Hannah De los Santos [aut], Emily Collins [aut], Kristin Bennett [aut], Jennifer Hurley [aut, cre], R Development Core Team [aut]
Maintainer: Jennifer Hurley <hurlej2@rpi.edu>
Repository: CRAN
Date/Publication: 2020-06-10 19:50:14 UTC

echo.find: Provides a function (echo_find) designed to find rhythms from data using extended harmonic oscillators.

Description

To read more about our inital work on this project and cite us, see Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations by H. De los Santos et al. (2017)

Function to calculate the results for all genes using the extended circadian harmonic oscillator (ECHO) method.

Description

Function to calculate the results for all genes using the extended circadian harmonic oscillator (ECHO) method.

Usage

echo_find(genes, begin, end, resol, num_reps, low = 1, high = 2,
  run_all_per, paired, rem_unexpr, rem_unexpr_amt = 70,
  rem_unexpr_amt_below = 0, is_normal, is_de_linear_trend, is_smooth,
  run_conf = F, which_conf = "Bootstrap", harm_cut = 0.03,
  over_cut = 0.15, seed = 30)

Arguments

genes

data frame of genes with the following specifications: first row is column labels, first column has gene labels/names, and all other columns have expression data. This expression data must be ordered by time point then by replicate, and must have evenly spaced time points. Any missing data must have cells left blank.

begin

first time point for dataset

end

last time point for dataset

resol

resolution of time points

num_reps

number of replicates

low

lower limit when looking for rhythms, in hours. May be unused if finding rhythms of any length within timecouse (run_all_per is TRUE).

high

upper limit when looking for rhythms, in hours. May be unused if finding rhythms of any length within timecouse (run_all_per is TRUE).

run_all_per

boolean which indicates whether or not rhythms of any length within timecourse should be searched for.

paired

if replicate data, whether the replicates are related (paired) or not (unpaired)

rem_unexpr

boolean indicating whether genes with less than rem_unexpr_amt percent expression should not be considered

rem_unexpr_amt

percentage of expression for which genes should not be considered if rem_unexpr is TRUE

rem_unexpr_amt_below

cutoff for expression

is_normal

boolean that indicates whether data should be normalized or not

is_de_linear_trend

boolean that indicates whether linear trends should be removed from data or not

is_smooth

boolean that indicates whether data should be smoothed or not

run_conf

boolean of whether or not to run confidence intervals

which_conf

string of which type of confidence interval to compute ("Bootstrap" or "Jackknife")

harm_cut

postive number indicating the cutoff for a gene to be considered harmonic

over_cut

postive number indicating the cutoff for a gene to be considered repressed/overexpressed

seed

number for random seed to fix for bootstrapping for confidence intervals

Value

results, a data frame which contains:

Gene Name

gene name

Convergence

depreciated result, always 0, will be removed in future versions

Iterations

depreciated result, always 0, will be removed in future versions

Amplitude.Change.Coefficient

Amplitude change coefficient value for fit

Oscillation Type

Type of oscillation (damped, driven, etc.)

Initial.Amplitude

Initial amplitude value for fit

Radian.Frequency

Radian frequency for fit

Period

Period for fit (in time units)

Phase Shift

Phase shift for fit (radians)

Hours Shifted

Phase shift for fit (hours)

Equilibrium Value

Equilibrium shift for fit

Slope

Slope value of original data, if linear baseline is removed

Tau

Kendall's tau between original and fitted values

P-value

P-value calculated based on Kendall's tau

BH Adj P-Value

Benjamini-Hochberg adjusted p-values

BY Adj P-Value

Benjamini-Yekutieli adjusted p-values

CI.PARAM.Low

Lower confidence interval bound for all parameters, if calculated

CI.PARAM.High

Higher confidence interval bound for all parameters, if calculated

Original TPX.Y

Processed values for gene expression at time point X, replicate Y

Fitted TPX

Fitted values for gene expression at time point X

Examples

# for more elaboration, please see the vignette
# "expressions" is the example echo.find data frame
 # long example - commented out
echo_find(genes = expressions, begin = 2, end = 48, resol = 2,
  num_reps = 3, low = 20, high = 26, run_all_per = FALSE,
  paired = FALSE, rem_unexpr = FALSE, rem_unexpr_amt = 70, rem_unexpr_amt_below=0,
  is_normal = FALSE, is_de_linear_trend = FALSE, is_smooth = FALSE)

Synthetic expression data for 12 genes.

Description

A dataset containing the names and expression values for 12 synthetically generated samples. This example data has time points from 2 to 48 hours with 2 hour resolution and 3 replicates. Random missing data is also included. Synthetic data was created by randomly selecting parameters for the extended harmonic oscillator equation (see journal paper link in vignette for the equation), then adding random uniform noise to each expression.

Usage

expressions

Format

A data frame with 12 rows and 73 variables (column 1: sample labels, columns to 2 to 73: numerical values for gene expression in the forsmat CTX.Y (time point X, replicate Y)).

Details

Note the data format: its first column first column has gene labels/names, and all other columns have expression data. This expression data is ordered by time point then by replicate, and has evenly spaced time points. Any missing data has cells left blank.