Description Usage Arguments Details Value References Examples
This is a function that takes use of Lomb-Scargle to detect rhythmic signals from time-series datasets containing individual information.
1 2 3 4 5 6 7 | meta3d(datafile, designfile, outdir = "cirout", filestyle, design_libColm,
design_subjectColm, minper = 20, maxper = 28, timeUnit = "hour",
design_hrColm, design_dayColm = NULL, design_minColm = NULL,
design_secColm = NULL, design_groupColm = NULL,
design_libIDrename = NULL, adjustedPhase = "predictedPer",
weightedMethod = TRUE, combinePvalue = "fisher",
outIntegrationFile = "both", dayZeroBased = FALSE, outSymbol = "")
|
datafile |
a character string. The name of data file containing time-sereis experimental values of all individuals. |
designfile |
a character string. The name of experimental design file,
at least containing the library ID(column names of |
outdir |
a character string. The name of directory used to store output files. |
filestyle |
a character vector(length 1 or 3). The data format of
input files, must be |
design_libColm |
a numeric value. The order index(from left to right)
of the column storing library ID in |
design_subjectColm |
a numeric value. The order index(from left to
right) of the column storing subject ID in |
minper |
a numeric value. The minimum period length of interested
rhythms. The default is |
maxper |
a numeric value. The maximum period length of interested
rhythms. The default is |
timeUnit |
a character string. The basic time-unit, must be one of
|
design_hrColm |
a numeric value. The order index(from left to right)
of the column storing time point value-sampling hour information in
|
design_dayColm |
a numeric value. The order index(from left to right)
of the column storing time point value-sampling day information in
|
design_minColm |
a numeric value. The order index(from left to right)
of the column storing time point value-sampling minute information in
|
design_secColm |
a numeric value. The order index(from left to right)
of the column storing time point value-sampling second information in
|
design_groupColm |
a numeric value. The order index(from left to
right) of the column storing experimental group information of each
individual in |
design_libIDrename |
a character vector(length 2) containing a
matchable character string in each library ID of |
adjustedPhase |
a character string. The method used to adjust each
phase calculated by Lomb-Scargle before getting integrated phase,
must be one of |
weightedMethod |
logical. If |
combinePvalue |
a character string. The method used to integrate
p-values of multiple individuals, currently only |
outIntegrationFile |
a character string. This parameter controls what
kinds of analysis results will be outputted, must be one of |
dayZeroBased |
logical. If |
outSymbol |
a character string. A common prefix exists in the names of output files. |
This function is originally aimed to analyze large scale perodic data with
individual information. Please pay attention to the data format of
datafile
and designfile
(see Examples
part).
Time-series experimental values(missing values as NA
) from
all individuals shoud be stored in datafile
, with the first row
containing all library ID(unique identification number for each sample)
and the first column containing all detected molecular names(eg.
transcript ID or gene name). The designfile
should at least have
three columns-library ID, subject ID and sampling time collumn.
Experimental group information of each subject ID may be in another
column. In addition, sampling time information may be stored in multiple
columns instead of one column. For example, sampling time-"36 hours" may
be recorded as "day 2"(sampling day column, design_dayColm
) plus
"12 hours"(sampling hour column, design_hrColm
). The library ID
in datafile
and designfile
should be same. If there are
different characters between library ID in these two files, try
design_libIDrename
to keep them same.
Lomb-Scargle(Glynn, 2006) is used to analyze time-series profiles
individual by individual. The original code is modified and added with
calculating baseline value and amplitude(using similar method
as meta2d
). Then p-values, period, phase, baseline
value, amplitude and relative amplitude from multiple individuals are
integrated group by group. P-values from different individuals are
integrated with Fisher's method("fisher"
) (Fisher,1925;
implementation code from MADAM). The integrated period, baseline
value, amplitude and relative amplitude are arithmetic mean of multiple
individuals, respectively. The integrated phase is
mean of circular quantities(adjustedPhase = "predictedPer"
) or
a arithmetic mean(adjustedPhase = "notAdjusted"
) of multiple
individual phases. If weightedMethod = TRUE
is selected, weighted
scores(-log10(p-values)
) will be taken into account in calculation
of integrated period, phase, baseline, amplitude and relative amplitude.
For completly removing the potential problem of averaging phases with
quite different period length(also mentioned in meta2d
),
setting minper
and maxper
to a same value may be the only
known way. For short time-series profiles(eg. 10 time points or less),
p-values given by Lomb-Scargle may be over conservative, which will also
lead to conservative integrated p-values. In such case, selecting a
proper p-value cut-off based on the p-value distribution is suggested.
meta3d
will write analysis results to outdir
instead of
returning them as objects. Output files with "LSresultSubjectID" in
the file name are Lomb-Scargle analysis results for each individual.
Files named with "CirCaseIntegrationGroupID" store integrated p-values,
period, phase, baseline, amplitude and relative amplitude values
from multiple individuals of each group and calculated FDR values based
on integrated p-values.
Glynn E. F., Chen J., and Mushegian A. R. (2006). Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics, 22(3), 310–316
Fisher, R.A. (1925). Statistical methods for research workers. Oliver and Boyd (Edinburgh).
Kugler K. G., Mueller L.A., and Graber A. (2010). MADAM - an open source toolbox for meta-analysis. Source Code for Biology and Medicine, 5, 3.
1 2 3 4 5 6 7 8 9 10 11 | # write 'cycHumanBloodData' and 'cycHumanBloodDesign' into two 'csv' files
write.csv(cycHumanBloodData, file="cycHumanBloodData.csv",
row.names=FALSE)
write.csv(cycHumanBloodDesign, file="cycHumanBloodDesign.csv",
row.names=FALSE)
# detect circadian transcripts in studied individuals
meta3d(datafile="cycHumanBloodData.csv",
designfile="cycHumanBloodDesign.csv", outdir="example", filestyle="csv",
design_libColm=1, design_subjectColm=2, design_hrColm=4,
design_groupColm=3)
|
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