Error when run transAnalysis

[quzhouxiachuan]

Hi, Error pops up when I was running transAnalysis, it worked fine when I was creating my_obj and running near_bait analysis, any idea what went wrong here? Thanks!

trans_results=transAnalysis(my_obj,k=20) [1] "Building adaptive windows..." [1] "Normalizing counts..." [1] "Generating synthetic samples...." [1] "Parameter estimation....."

Iter: 1 fn: -4341.3303 Pars: 0.29091570755 0.29097460123 0.41810969122 0.87304777458 0.09543519056 0.03151703535 0.00639120995 0.94256920951 0.05103958152 0.00526952945 0.08872967424 0.90600079721 0.30102996865 0.00000002563 2.01257263411 0.32112667846 2.72907602971 0.22943969412 Iter: 2 fn: -4341.3303 Pars: 0.29091570755 0.29097460123 0.41810969122 0.87304777458 0.09543519056 0.03151703535 0.00639120995 0.94256920951 0.05103958152 0.00526952945 0.08872967424 0.90600079721 0.30102996865 0.00000002563 2.01257263411 0.32112667846 2.72907602971 0.22943969412 solnp--> Completed in 2 iterations [1] "BED file of highest interacting domains for trans chromosomes are saved in /Users/yudeng/Desktop/LAB/Panos Lab/G6PD_results_R4Cker1/"

library(ggplot2) ggplot(trans_results$norm_counts_avg, aes(x=Coord, y=Count, colour=Condition))+

• theme_bw()+
• geom_line()+xlab(paste("Chromosome coordinates (", my_obj@bait_chr, ")", sep =""))+
• ylab("Normalized counts")+
• ggtitle(paste("cis bait analysis (", my_obj@bait_name, " bait)", sep = "")) Error in trans_results$norm_counts_avg : $ operator is invalid for atomic vectors

Thanks! I also attached my two input files here.

G6PD_hindiii1.bedGraph.txt [Uploading G6PD_hindiii2.bedGraph.txt…]()

[rr1859]

Hi,

We do not have the option to plot trans interactions in R - its only for near the bait and cis. I would recommend loading the bedGraph files in IGV to visualize the data.

[quzhouxiachuan]

Thanks for your quick response!