ARA and pyramid plots issues

[BERICP01]

Hello,

I am facing some issues when I try to use ARA and pyramid plot functions.

For the ARA here is my script:

**library(GENOVA)
library(rhdf5)
library(strawr)

setwd('/gpfs/data/HernandoLab/home/bericp01/HiC/results/ARA')
dir <- '/gpfs/data/HernandoLab/home/bericp01/HiC/results/ARA'

CTRL_10kb_juicer <- readRDS("/gpfs/data/HernandoLab/home/bericp01/HiC/results/cis-quantification/CTRL_10kb_juicer.rds")
CHD7_10kb_juicer <- readRDS("/gpfs/data/HernandoLab/home/bericp01/HiC/results/cis-quantification/CHD7_10kb_juicer.rds")
CTRL_CHD7 <- sync_indices(list(CTRL_10kb_juicer, CHD7_10kb_juicer))
CHD7_peaks <- read.delim('/gpfs/data/HernandoLab/home/bericp01/HiC/MACS2/bedtools_Intersect_CHD7.bed')

CTRL_CHD7_ARA <- ARA(CTRL_CHD7,
bed = CHD7_peaks[,1:3],
shift = 1e+06)
pdf(file.path(dir, "ARA_CHD7.pdf"))
visualise(CTRL_CHD7_ARA,
title = "ARA 501mel sgCHD7",
colour_lim = c(0, 40), colour_lim_contrast = c(-5, 5),
metric = "diff",
contrast = 1)
dev.off()
quantifyARA_chd7 <- quantify(CTRL_CHD7_ARA)
pdf(file.path(dir, "ARA_CHD7_boxplot.pdf"))
boxplot(split(quantifyARA_chd7$per_loop$foldchange,
f = quantifyARA_chd7$per_loop$sample),
col = c('red', 'darkgrey'), outline = F,
ylab = 'pixel enrichment extended loops')
dev.off()**

Then I get this error:
Error in value[[1L]] : subscript out of bounds
Calls: ARA -> anchors_ARA -> bed2idx -> unsplit -> is.data.frame
Execution halted

With the pyramid plot the script is:

**library(GENOVA)
library(rhdf5)
library(strawr)

setwd('/gpfs/data/HernandoLab/home/bericp01/HiC/results/Plots')
dir <- '/gpfs/data/HernandoLab/home/bericp01/HiC/results/Plots'
bed <- '/gpfs/data/HernandoLab/home/bericp01/genome_references/GENCODE_v44_Hg38.bed'

MELANOCYTIC_10kb_juicer <- readRDS("/gpfs/data/HernandoLab/home/bericp01/HiC/results/cis-quantification/MELANOCYTIC_10kb_juicer.rds")
MESENCHYMAL_10kb_juicer <- readRDS("/gpfs/data/HernandoLab/home/bericp01/HiC/results/cis-quantification/MESENCHYMAL_10kb_juicer.rds")

#Region TFAP2A
pdf(file.path(dir, "HiC_diff_MEL_MES_TFAP2A.pdf"))
pyramid_difference(exp1 = MELANOCYTIC_10kb_juicer,
exp2 = MESENCHYMAL_10kb_juicer,
coplot = 'diff',
chrom = "chr6:9,700,000-10,800,000", cut.off = 50, genes = bed)
dev.off()**

Then I get this error:
Error in standardise_location(chrom, start, end, singular = TRUE) :
could not find function "standardise_location"
Calls: pyramid_difference
Execution halted

Any help would be extremely appreciate!
Thanks
Pietro

[teunbrand]

I don't know where to begin debugging this. Can you please provide a minimal reproducible example instead of pasting entire scripts? Preferably using the data provided in get_test_data() funciton.