Hey,

I'm very new to R.

I've been analyzing ChIP-seq data using MACS2 and the output for predictd is an R script.

For some reason it doesn't work and I've noticed that the variable turns black in the middle while the rest is blue (picture attached).

What does it mean?

Thank you!

image|459x111

Hi,

I'm not 100% sure on this but I think the blue numbers represents labels attached to the variables, not actual values.

Any chance you could make a reprex (Reproducible Example) to give us more info?

Hey! Thanks for replying.

I'll paste the script:

(note that for p, m, xcorr and ycorr there are a lot more numbers attached (I deleted most due to character limit)

p <- c(0.0439358309282,0.0512188757622,0...)

m <- c(0.0453688730178,0.0529371005383...)

ycorr <- c(5.700878250599218e-05...)

xcorr <- c(-600.0,-598.999165971643...)

altd <- c(4, 292)

x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)

pdf('predictd_model.pdf',height=6,width=6)

plot(x,p,type='l',col=c('red'),main='Peak Model',xlab='Distance to the middle',ylab='Percentage')

lines(x,m,col=c('blue'))

legend('topleft',c('forward tags','reverse tags'),lty=c(1,1,1),col=c('red','blue'))

plot(xcorr,ycorr,type='l',col=c('black'),main='Cross-Correlation',xlab='Lag between + and - tags',ylab='Correlation')

abline(v=altd,lty=2,col=c('red'))

legend('topleft','alternative lag(s)',lty=2,col='red')

legend('right','alt lag(s) : 4,292',bty='n')

dev.off()

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