source("/home/yzizhen/chip_seq/R_script/motifRG/inst/Scripts/analysis.R")
source("/home/yzizhen/chip_seq/R_script/motifRG/inst/Scripts/analysis.R")
q()
n
data(control)
ls()
head(control.seq)
dim(control.seq)
length(control.seq)
save(control.seq[1:10000], file="control.rda")
head(control.seq[1:10000])
control.seq <- control.seq[1:10000]
ls()
 ctcf.seq <- DNAStringSet(getsequence(ctcf[1:10000,]))
head(ctcf)
 ctcf.seq <- DNAStringSet(getsequence(ctcf[1:10000,]))
head(ctcf)
 ctcf.seq <- DNAStringSet(getsequence(ctcf[1:10000,]))
head(ctcf)
library(Biostring)
library(Biostrings)
 ctcf.seq <- DNAStringSet(getsequence(ctcf[1:10000,]))
 ctcf.seq <- DNAStringSet(getsequence(ctcf[1:10000,]))
save(ctcf.seq, file="ctcf.rda")
save(control.seq, file="control.rda")
save(ctcf.seq, file="ctcf.seq.rda")
save(control.seq, file="control.seq.rda")
traceback()
source("/home/yzizhen/chip_seq/R_script/motifRG/R/motif.rg.R")
ctct.motifs$summary
ctcf.motifs$summary
?xaxt
?plot.default
?plot
options(error=recover)
source("/home/yzizhen/chip_seq/R_script/motifRG/R/motif.rg.R")
plotMotif(ctcf.motifs$match[[1]])
1
xaxt
0
0
?plot
?plot.default
?par
source("/home/yzizhen/chip_seq/R_script/motifRG/R/motif.rg.R")
plotMotif(ctcf.motifs$match[[1]])
ctcf.motif$summary
ctcf.motifs$summary
IUPAC_CODE_MAP
plotMotif(ctcf.motifs$match[[1]])
X11()
ctcf.motifs$summary
plotMotif(ctcf.motifs$match[[2]])
table(ctcf.motifs$fg.counts[,1:2])
table(ctcf.motifs$fg.counts[,1], ctcf.motifs$fg.counts[,2])
q()
n
ctcf.seq
control.seq
all.seq <- append(ctcf.seq, control.seq)
all.seq
ctcf.motifs$summary
ctcf.motifs$summary
?findMotif
q(0
)
q()
n
source("analysis.R")
names(pwm.match.extend)
names(pwm.match.extend$match)
q()
n
