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R/datasetsinfo.R
In MetaCycle: Evaluate Periodicity in Large Scale Data
##' @name cycMouseLiverRNA
##' @title cycMouseLiverRNA
##' @description This data set lists expression profiles of 10 circadian
##' transcripts with 1h-resolution covering two days.
##' @docType data
##' @usage cycMouseLiverRNA
##' @format A dataframe containing 49 columns(column 1 = transcript name,
##' column 2 to 49 = time points from CT18 to CT65).
##' @source Hughes M. E., et al. (2009). Harmonics of circadian gene
##' transcription in mammals. \emph{PLoS Genet}, \bold{5(4)}, e1000442.
NULL
##' @name cycMouseLiverProtein
##' @title cycMouseLiverProtein
##' @description This data set lists expression profiles of 5 circadian
##' proteins with 3h-resolution covering two days.
##' @docType data
##' @usage cycMouseLiverProtein
##' @format A dataframe containing 49 columns(column 1 = protein name,
##' column 2 to 49 = time points from CT0 to CT45 with three replicates
##' at each time point).
##' @source Robles M. S., Cox J., Mann M. (2014). In-vivo quantitative
##' proteomics reveals a key contribution of post-transcriptional
##' mechanisms to the circadian regulation of liver metabolism.
##' \emph{PLoS Genet}, \bold{10(1)}, e1004047.
NULL
##' @name cycSimu4h2d
##' @title cycSimu4h2d
##' @description This data set lists 20 simulated profiles(periodic and
##' non-periodic) with 4h-resolution covering two periods.
##' @docType data
##' @usage cycSimu4h2d
##' @format A dataframe containing 13 columns(column 1 = curve ID, column 2 to
##' 13 = time points from 0 to 44).
##' @source Wu G., Zhu J., Yu J., Zhou L., Huang J. Z. and Zhang Z. (2014).
##' Evaluation of five methods for genome-wide circadian gene identification.
##' \emph{Journal of Biological Rhythms}, \bold{29(4)}, 231--242.
NULL
##' @name cycYeastCycle
##' @title cycYeastCycle
##' @description This data set lists expression profiles of 10 cycling
##' transcripts with 16-minutes resolution covering about two yeast cell
##' cycles.
##' @docType data
##' @usage cycYeastCycle
##' @format A dataframe containing 12 columns(column 1 = transcript name,
##' column 2 to 12 = time points from 2 minutes to 162 minutes after
##' recovery phase).
##' @source Orlando D. A., et al. (2008). Global control of cell-cycle
##' transcription by coupled CDK and network oscillators. \emph{Nature},
##' \bold{453(7197)}, 944--947.
NULL
##' @name cycVignettesAMP
##' @title cycVignettesAMP
##' @description This data set lists meta2d's analysis results of three
##' circadian transcripts selected from the same source dataset used by
##' cycMouseLiverRNA.
##' @docType data
##' @usage cycVignettesAMP
##' @format A dataframe containing 71 columns described as below:
##' \tabular{rlll}{
##' [,1] \tab CycID \tab character \tab transcript name\cr
##' [,2] \tab ARS_pvalue \tab numeric \tab pvalue from ARS\cr
##' [,3] \tab ARS_BH.Q \tab numeric \tab FDR from ARS\cr
##' [,4] \tab ARS_period \tab numeric \tab period from ARS\cr
##' [,5] \tab ARS_adjphase \tab numeric \tab adjusted phase from ARS\cr
##' [,6] \tab ARS_amplitude \tab numeric \tab amplitude from ARS\cr
##' [,7] \tab JTK_pvalue \tab numeric \tab pvalue from JTK\cr
##' [,8] \tab JTK_BH.Q \tab numeric \tab FDR from JTK\cr
##' [,9] \tab JTK_period \tab numeric \tab period from JTK\cr
##' [,10] \tab JTK_adjphase \tab numeric \tab adjusted phase from JTK\cr
##' [,11] \tab JTK_amplitude \tab numeric \tab amplitude from JTK\cr
##' [,12] \tab LS_pvalue \tab numeric \tab pvalue from LS\cr
##' [,13] \tab LS_BH.Q \tab numeric \tab FDR from JTK\cr
##' [,14] \tab LS_period \tab numeric \tab period from LS\cr
##' [,15] \tab LS_adjphase \tab numeric \tab adjusted phase from LS\cr
##' [,16] \tab LS_amplitude \tab numeric \tab amplitude from LS\cr
##' [,17] \tab meta2d_pvalue \tab numeric \tab integrated pvalue\cr
##' [,18] \tab meta2d_BH.Q \tab numeric \tab FDR based on integrated pvalue\cr
##' [,19] \tab meta2d_period \tab numeric \tab averaged period of three methods\cr
##' [,20] \tab meta2d_phase \tab numeric \tab integrated phase\cr
##' [,21] \tab meta2d_Base \tab numeric \tab baseline value given by meta2d\cr
##' [,22] \tab meta2d_AMP \tab numeric \tab amplitude given by meta2d\cr
##' [,23] \tab meta2d_rAMP \tab numeric \tab relative amplitude\cr
##' [,24:71] \tab CT18 to CT65 \tab numeric \tab sampling time point
##' }
##' @source Hughes M. E., et al. (2009). Harmonics of circadian gene
##' transcription in mammals. \emph{PLoS Genet}, \bold{5(4)}, e1000442.
NULL
##' @name cycHumanBloodData
##' @title cycHumanBloodData
##' @description This data set lists time-series profiles of 10 transcripts
##' sampled from multiple individuals under different sleep conditions.
##' @docType data
##' @usage cycHumanBloodData
##' @format A dataframe containing 439 columns (column 1 = transcript name,
##' column 2 to 439 = samples from individuals at different time points and
##' sleep conditions).
##' @source Moller-Levet C. S., et al. (2013). Effects of insufficient sleep on
##' circadian rhythmicity and expression amplitude of the human blood
##' transcriptome. \emph{Proc Natl Acad Sci U S A}, \bold{110(12)},
##' E1132--1141.
NULL
##' @name cycHumanBloodDesign
##' @title cycHumanBloodDesign
##' @description This data set describes individual information, sleep
##' condition and sampling time corresponding to each sample in
##' 'cycHumanBloodData'.
##' @docType data
##' @usage cycHumanBloodDesign
##' @format A dataframe containing 4 columns described as below:
##' \tabular{rlll}{
##' [,1] \tab sample_library \tab character \tab sample ID\cr
##' [,2] \tab subject \tab character \tab individual ID\cr
##' [,3] \tab group \tab character \tab sleep condition\cr
##' [,4] \tab time_hoursawake \tab numeric \tab hours after awake
##' }
##' @source Moller-Levet C. S., et al. (2013). Effects of insufficient sleep on
##' circadian rhythmicity and expression amplitude of the human blood
##' transcriptome. \emph{Proc Natl Acad Sci U S A}, \bold{110(12)},
##' E1132--1141.
NULL
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##' @name cycMouseLiverRNA
##' @title cycMouseLiverRNA
##' @description This data set lists expression profiles of 10 circadian
##' transcripts with 1h-resolution covering two days.
##' @docType data
##' @usage cycMouseLiverRNA
##' @format A dataframe containing 49 columns(column 1 = transcript name,
##' column 2 to 49 = time points from CT18 to CT65).
##' @source Hughes M. E., et al. (2009). Harmonics of circadian gene
##' transcription in mammals. \emph{PLoS Genet}, \bold{5(4)}, e1000442.
NULL
##' @name cycMouseLiverProtein
##' @title cycMouseLiverProtein
##' @description This data set lists expression profiles of 5 circadian
##' proteins with 3h-resolution covering two days.
##' @docType data
##' @usage cycMouseLiverProtein
##' @format A dataframe containing 49 columns(column 1 = protein name,
##' column 2 to 49 = time points from CT0 to CT45 with three replicates
##' at each time point).
##' @source Robles M. S., Cox J., Mann M. (2014). In-vivo quantitative
##' proteomics reveals a key contribution of post-transcriptional
##' mechanisms to the circadian regulation of liver metabolism.
##' \emph{PLoS Genet}, \bold{10(1)}, e1004047.
NULL
##' @name cycSimu4h2d
##' @title cycSimu4h2d
##' @description This data set lists 20 simulated profiles(periodic and
##' non-periodic) with 4h-resolution covering two periods.
##' @docType data
##' @usage cycSimu4h2d
##' @format A dataframe containing 13 columns(column 1 = curve ID, column 2 to
##' 13 = time points from 0 to 44).
##' @source Wu G., Zhu J., Yu J., Zhou L., Huang J. Z. and Zhang Z. (2014).
##' Evaluation of five methods for genome-wide circadian gene identification.
##' \emph{Journal of Biological Rhythms}, \bold{29(4)}, 231--242.
NULL
##' @name cycYeastCycle
##' @title cycYeastCycle
##' @description This data set lists expression profiles of 10 cycling
##' transcripts with 16-minutes resolution covering about two yeast cell
##' cycles.
##' @docType data
##' @usage cycYeastCycle
##' @format A dataframe containing 12 columns(column 1 = transcript name,
##' column 2 to 12 = time points from 2 minutes to 162 minutes after
##' recovery phase).
##' @source Orlando D. A., et al. (2008). Global control of cell-cycle
##' transcription by coupled CDK and network oscillators. \emph{Nature},
##' \bold{453(7197)}, 944--947.
NULL
##' @name cycVignettesAMP
##' @title cycVignettesAMP
##' @description This data set lists meta2d's analysis results of three
##' circadian transcripts selected from the same source dataset used by
##' cycMouseLiverRNA.
##' @docType data
##' @usage cycVignettesAMP
##' @format A dataframe containing 71 columns described as below:
##' \tabular{rlll}{
##' [,1] \tab CycID \tab character \tab transcript name\cr
##' [,2] \tab ARS_pvalue \tab numeric \tab pvalue from ARS\cr
##' [,3] \tab ARS_BH.Q \tab numeric \tab FDR from ARS\cr
##' [,4] \tab ARS_period \tab numeric \tab period from ARS\cr
##' [,5] \tab ARS_adjphase \tab numeric \tab adjusted phase from ARS\cr
##' [,6] \tab ARS_amplitude \tab numeric \tab amplitude from ARS\cr
##' [,7] \tab JTK_pvalue \tab numeric \tab pvalue from JTK\cr
##' [,8] \tab JTK_BH.Q \tab numeric \tab FDR from JTK\cr
##' [,9] \tab JTK_period \tab numeric \tab period from JTK\cr
##' [,10] \tab JTK_adjphase \tab numeric \tab adjusted phase from JTK\cr
##' [,11] \tab JTK_amplitude \tab numeric \tab amplitude from JTK\cr
##' [,12] \tab LS_pvalue \tab numeric \tab pvalue from LS\cr
##' [,13] \tab LS_BH.Q \tab numeric \tab FDR from JTK\cr
##' [,14] \tab LS_period \tab numeric \tab period from LS\cr
##' [,15] \tab LS_adjphase \tab numeric \tab adjusted phase from LS\cr
##' [,16] \tab LS_amplitude \tab numeric \tab amplitude from LS\cr
##' [,17] \tab meta2d_pvalue \tab numeric \tab integrated pvalue\cr
##' [,18] \tab meta2d_BH.Q \tab numeric \tab FDR based on integrated pvalue\cr
##' [,19] \tab meta2d_period \tab numeric \tab averaged period of three methods\cr
##' [,20] \tab meta2d_phase \tab numeric \tab integrated phase\cr
##' [,21] \tab meta2d_Base \tab numeric \tab baseline value given by meta2d\cr
##' [,22] \tab meta2d_AMP \tab numeric \tab amplitude given by meta2d\cr
##' [,23] \tab meta2d_rAMP \tab numeric \tab relative amplitude\cr
##' [,24:71] \tab CT18 to CT65 \tab numeric \tab sampling time point
##' }
##' @source Hughes M. E., et al. (2009). Harmonics of circadian gene
##' transcription in mammals. \emph{PLoS Genet}, \bold{5(4)}, e1000442.
NULL
##' @name cycHumanBloodData
##' @title cycHumanBloodData
##' @description This data set lists time-series profiles of 10 transcripts
##' sampled from multiple individuals under different sleep conditions.
##' @docType data
##' @usage cycHumanBloodData
##' @format A dataframe containing 439 columns (column 1 = transcript name,
##' column 2 to 439 = samples from individuals at different time points and
##' sleep conditions).
##' @source Moller-Levet C. S., et al. (2013). Effects of insufficient sleep on
##' circadian rhythmicity and expression amplitude of the human blood
##' transcriptome. \emph{Proc Natl Acad Sci U S A}, \bold{110(12)},
##' E1132--1141.
NULL
##' @name cycHumanBloodDesign
##' @title cycHumanBloodDesign
##' @description This data set describes individual information, sleep
##' condition and sampling time corresponding to each sample in
##' 'cycHumanBloodData'.
##' @docType data
##' @usage cycHumanBloodDesign
##' @format A dataframe containing 4 columns described as below:
##' \tabular{rlll}{
##' [,1] \tab sample_library \tab character \tab sample ID\cr
##' [,2] \tab subject \tab character \tab individual ID\cr
##' [,3] \tab group \tab character \tab sleep condition\cr
##' [,4] \tab time_hoursawake \tab numeric \tab hours after awake
##' }
##' @source Moller-Levet C. S., et al. (2013). Effects of insufficient sleep on
##' circadian rhythmicity and expression amplitude of the human blood
##' transcriptome. \emph{Proc Natl Acad Sci U S A}, \bold{110(12)},
##' E1132--1141.
NULL
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