22. Kc167 and S2 cell loops aggregation at 4 types of gene - ZhengmzLab/roX2-RDD-Data-Analysis-Strategy GitHub Wiki

The intra-genes of roX2 RDD from [Section 16](#16) are divided to 41 bins by makewindows() function of BEDTools, after extended 50 percent of the isoform length on both sides. Next, create bin-bin pairs in each isoform after a PET count threshold, and overlap with both anchors of loops, to count sums of PET count of loops to generate a matrix of bin-bin with PET-count-sum. Finally, after calculating the RPKM, RPKMs from Kc167 and S2 roX2 RDD libraries are used for drawing their boxplots of gene express levels respectively, based on the 4 types of genes. Two-sample Wilcoxon test for genes is performed in each plots using wilcox.test() function of R package stats. The middle line of a boxplot denotes median; box boundary encloses interquartile range (IQR); and whiskers denote 1.5× IQR, draw by R package ggplot2.