cycVignettesAMP

<p>This data set lists meta2d's analysis results of three
  circadian transcripts selected from the same source dataset used by
  cycMouseLiverRNA.</p>

There are two functions-meta2d and meta3d for
detecting rhythmic signals from time-series datasets. For analyzing
time-series datasets without individual information, 'meta2d' is
suggested, which could incorporates multiple methods from ARSER,
JTK_CYCLE and Lomb-Scargle in the detection of interested rhythms. For
analyzing time-series datasets with individual information, 'meta3d' is
suggested, which takes use of any one of these three methods to analyze
time-series data individual by individual and gives out integrated values
based on analysis result of each individual.

Gang Wu

MetaCycle

Evaluate Periodicity in Large Scale Data

Ron Anafi

John Hogenesch

Michael Hughes

Karl Kornacker

Xavier Li

Matthew Carlucci

cycVignettesAMP function

<p>A dataframe containing 71 columns described as below:</p><table class="table">
<tr><td>[,1]</td><td>CycID</td><td>character</td><td>transcript name</td></tr>
<tr><td>[,2]</td><td>ARS_pvalue</td><td>numeric</td><td>pvalue from ARS</td></tr>
<tr><td>[,3]</td><td>ARS_BH.Q</td><td>numeric</td><td>FDR from ARS</td></tr>
<tr><td>[,4]</td><td>ARS_period</td><td>numeric</td><td>period from ARS</td></tr>
<tr><td>[,5]</td><td>ARS_adjphase</td><td>numeric</td><td>adjusted phase from ARS</td></tr>
<tr><td>[,6]</td><td>ARS_amplitude</td><td>numeric</td><td>amplitude from ARS</td></tr>
<tr><td>[,7]</td><td>JTK_pvalue</td><td>numeric</td><td>pvalue from JTK</td></tr>
<tr><td>[,8]</td><td>JTK_BH.Q</td><td>numeric</td><td>FDR from JTK</td></tr>
<tr><td>[,9]</td><td>JTK_period</td><td>numeric</td><td>period from JTK</td></tr>
<tr><td>[,10]</td><td>JTK_adjphase</td><td>numeric</td><td>adjusted phase from JTK</td></tr>
<tr><td>[,11]</td><td>JTK_amplitude</td><td>numeric</td><td>amplitude from JTK</td></tr>
<tr><td>[,12]</td><td>LS_pvalue</td><td>numeric</td><td>pvalue from LS</td></tr>
<tr><td>[,13]</td><td>LS_BH.Q</td><td>numeric</td><td>FDR from JTK</td></tr>
<tr><td>[,14]</td><td>LS_period</td><td>numeric</td><td>period from LS</td></tr>
<tr><td>[,15]</td><td>LS_adjphase</td><td>numeric</td><td>adjusted phase from LS</td></tr>
<tr><td>[,16]</td><td>LS_amplitude</td><td>numeric</td><td>amplitude from LS</td></tr>
<tr><td>[,17]</td><td>meta2d_pvalue</td><td>numeric</td><td>integrated pvalue</td></tr>
<tr><td>[,18]</td><td>meta2d_BH.Q</td><td>numeric</td><td>FDR based on integrated pvalue</td></tr>
<tr><td>[,19]</td><td>meta2d_period</td><td>numeric</td><td>averaged period of three methods</td></tr>
<tr><td>[,20]</td><td>meta2d_phase</td><td>numeric</td><td>integrated phase</td></tr>
<tr><td>[,21]</td><td>meta2d_Base</td><td>numeric</td><td>baseline value given by meta2d</td></tr>
<tr><td>[,22]</td><td>meta2d_AMP</td><td>numeric</td><td>amplitude given by meta2d</td></tr>
<tr><td>[,23]</td><td>meta2d_rAMP</td><td>numeric</td><td>relative amplitude</td></tr>
<tr><td>[,24:71]</td><td>CT18 to CT65</td><td>numeric</td><td>sampling time point</td></tr>
</table><p></p><p></p>

Format

cycVignettesAMP — cycVignettesAMP

<p>A dataframe containing 71 columns described as below:</p><table class='table'>
<tr><td>[,1]</td><td>CycID</td><td>character</td><td>transcript name</td></tr>
<tr><td>[,2]</td><td>ARS_pvalue</td><td>numeric</td><td>pvalue from ARS</td></tr>
<tr><td>[,3]</td><td>ARS_BH.Q</td><td>numeric</td><td>FDR from ARS</td></tr>
<tr><td>[,4]</td><td>ARS_period</td><td>numeric</td><td>period from ARS</td></tr>
<tr><td>[,5]</td><td>ARS_adjphase</td><td>numeric</td><td>adjusted phase from ARS</td></tr>
<tr><td>[,6]</td><td>ARS_amplitude</td><td>numeric</td><td>amplitude from ARS</td></tr>
<tr><td>[,7]</td><td>JTK_pvalue</td><td>numeric</td><td>pvalue from JTK</td></tr>
<tr><td>[,8]</td><td>JTK_BH.Q</td><td>numeric</td><td>FDR from JTK</td></tr>
<tr><td>[,9]</td><td>JTK_period</td><td>numeric</td><td>period from JTK</td></tr>
<tr><td>[,10]</td><td>JTK_adjphase</td><td>numeric</td><td>adjusted phase from JTK</td></tr>
<tr><td>[,11]</td><td>JTK_amplitude</td><td>numeric</td><td>amplitude from JTK</td></tr>
<tr><td>[,12]</td><td>LS_pvalue</td><td>numeric</td><td>pvalue from LS</td></tr>
<tr><td>[,13]</td><td>LS_BH.Q</td><td>numeric</td><td>FDR from JTK</td></tr>
<tr><td>[,14]</td><td>LS_period</td><td>numeric</td><td>period from LS</td></tr>
<tr><td>[,15]</td><td>LS_adjphase</td><td>numeric</td><td>adjusted phase from LS</td></tr>
<tr><td>[,16]</td><td>LS_amplitude</td><td>numeric</td><td>amplitude from LS</td></tr>
<tr><td>[,17]</td><td>meta2d_pvalue</td><td>numeric</td><td>integrated pvalue</td></tr>
<tr><td>[,18]</td><td>meta2d_BH.Q</td><td>numeric</td><td>FDR based on integrated pvalue</td></tr>
<tr><td>[,19]</td><td>meta2d_period</td><td>numeric</td><td>averaged period of three methods</td></tr>
<tr><td>[,20]</td><td>meta2d_phase</td><td>numeric</td><td>integrated phase</td></tr>
<tr><td>[,21]</td><td>meta2d_Base</td><td>numeric</td><td>baseline value given by meta2d</td></tr>
<tr><td>[,22]</td><td>meta2d_AMP</td><td>numeric</td><td>amplitude given by meta2d</td></tr>
<tr><td>[,23]</td><td>meta2d_rAMP</td><td>numeric</td><td>relative amplitude</td></tr>
<tr><td>[,24:71]</td><td>CT18 to CT65</td><td>numeric</td><td>sampling time point</td></tr>
</table>



cycVignettesAMP: cycVignettesAMP

Description

Usage

Arguments

Format

[,1]	CycID	character	transcript name
[,2]	ARS_pvalue	numeric	pvalue from ARS
[,3]	ARS_BH.Q	numeric	FDR from ARS
[,4]	ARS_period	numeric	period from ARS
[,5]	ARS_adjphase	numeric	adjusted phase from ARS
[,6]	ARS_amplitude	numeric	amplitude from ARS
[,7]	JTK_pvalue	numeric	pvalue from JTK
[,8]	JTK_BH.Q	numeric	FDR from JTK
[,9]	JTK_period	numeric	period from JTK
[,10]	JTK_adjphase	numeric	adjusted phase from JTK
[,11]	JTK_amplitude	numeric	amplitude from JTK
[,12]	LS_pvalue	numeric	pvalue from LS
[,13]	LS_BH.Q	numeric	FDR from JTK
[,14]	LS_period	numeric	period from LS
[,15]	LS_adjphase	numeric	adjusted phase from LS
[,16]	LS_amplitude	numeric	amplitude from LS
[,17]	meta2d_pvalue	numeric	integrated pvalue
[,18]	meta2d_BH.Q	numeric	FDR based on integrated pvalue
[,19]	meta2d_period	numeric	averaged period of three methods
[,20]	meta2d_phase	numeric	integrated phase
[,21]	meta2d_Base	numeric	baseline value given by meta2d
[,22]	meta2d_AMP	numeric	amplitude given by meta2d
[,23]	meta2d_rAMP	numeric	relative amplitude
[,24:71]	CT18 to CT65	numeric	sampling time point