Function to calculate the results for all genes using the extended circadian harmonic oscillator (ECHO) method.
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)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.
first time point for dataset
last time point for dataset
resolution of time points
number of replicates
lower limit when looking for rhythms, in hours. May be unused if finding rhythms of any length within timecouse (run_all_per is TRUE).
upper limit when looking for rhythms, in hours. May be unused if finding rhythms of any length within timecouse (run_all_per is TRUE).
boolean which indicates whether or not rhythms of any length within timecourse should be searched for.
if replicate data, whether the replicates are related (paired) or not (unpaired)
boolean indicating whether genes with less than rem_unexpr_amt percent expression should not be considered
percentage of expression for which genes should not be considered if rem_unexpr is TRUE
cutoff for expression
boolean that indicates whether data should be normalized or not
boolean that indicates whether linear trends should be removed from data or not
boolean that indicates whether data should be smoothed or not
boolean of whether or not to run confidence intervals
string of which type of confidence interval to compute ("Bootstrap" or "Jackknife")
postive number indicating the cutoff for a gene to be considered harmonic
postive number indicating the cutoff for a gene to be considered repressed/overexpressed
number for random seed to fix for bootstrapping for confidence intervals
results, a data frame which contains:
gene name
depreciated result, always 0, will be removed in future versions
depreciated result, always 0, will be removed in future versions
Amplitude change coefficient value for fit
Type of oscillation (damped, driven, etc.)
Initial amplitude value for fit
Radian frequency for fit
Period for fit (in time units)
Phase shift for fit (radians)
Phase shift for fit (hours)
Equilibrium shift for fit
Slope value of original data, if linear baseline is removed
Kendall's tau between original and fitted values
P-value calculated based on Kendall's tau
Benjamini-Hochberg adjusted p-values
Benjamini-Yekutieli adjusted p-values
Lower confidence interval bound for all parameters, if calculated
Higher confidence interval bound for all parameters, if calculated
Processed values for gene expression at time point X, replicate Y
Fitted values for gene expression at time point X
# NOT RUN {
# for more elaboration, please see the vignette
# "expressions" is the example echo.find data frame
# }
# NOT RUN {
# 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)
# }
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