-
Notifications
You must be signed in to change notification settings - Fork 15
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
ARA and pyramid plots issues #344
Comments
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 |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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
The text was updated successfully, but these errors were encountered: