使用MetaCycle进行生物节律基因分析

生物节律分析

library(MetaCycle)
head(cycMouseLiverRNA[,1:5])
cycMouseLiverRNA
write.csv(cycMouseLiverRNA, file="cycMouseLiverRNA.csv", row.names=FALSE)
# analyze 'cycMouseLiverRNA.csv' with JTK_CYCLE
# this is masked for keeping the total running time within 10s required by CRAN check
# meta2d(infile="cycMouseLiverRNA.csv", filestyle="csv", outdir="example",
# timepoints=18:65, cycMethod="JTK", outIntegration="noIntegration")
# analyze 'cycMouseLiverProtein.txt' with JTK_CYCLE and Lomb-Scargle
meta2d(infile="cycMouseLiverProtein.txt", filestyle="txt",outdir="example", timepoints=rep(seq(0, 45, by=3), each=3),
cycMethod=c("JTK","LS"), outIntegration="noIntegration")
# analyze 'cycSimu4h2d.csv' with ARSER, JTK_CYCLE and Lomb-Scargle and
# output integration file with analysis results from each method
meta2d(infile="cycSimu4h2d.csv", filestyle="csv", outdir="example",
timepoints="Line1")
# analyze 'cycYeastCycle.csv' with ARSER, JTK_CYCLE and Lomb-Scargle to
# detect transcripts associated with cell cycle, and only output
# integration file
meta2d(infile="cycYeastCycle.csv",filestyle="csv", outdir="example",
minper=80, maxper=96, timepoints=seq(2, 162, by=16),
outIntegration="onlyIntegration", ARSdefaultPer=85,
outRawData=TRUE)
# return analysis results instead of output them into files
cyc <- meta2d(infile="cycYeastCycle.csv",filestyle="csv",
minper=80, maxper=96, timepoints=seq(2, 162, by=16),
outputFile=FALSE, ARSdefaultPer=85, outRawData=TRUE)
head(cyc$ARS)
head(cyc$JTK)
head(cyc$LS)
head(cyc$meta)