Hi there, I am trying to run OmicsNetR to build an integrated network of my proteomic and metabolomic data. My code is shown below:
library(OmicsNetR)
rm(list = ls()) # Clear .GlobalEnv of your R session
# Initiate dataset object. Always do this beforehand
dataSet <- Init.Data()
# Prepare dataset (this is a small subset)
dataSet <- PrepareInputList(dataSet,
"#Uniprot logFC
A0A096MIV5 0.109442807
A0A096MIW7 -0.060478153
A0A096MIX1 -0.583380627
A0A096MIX2 0.019019237
A0A096MIZ1 -0.195203233",
"rno", "protein", "uniprot")
dataSet <- PrepareInputList(dataSet,
"#KEGG logFC
C00003 -0.046093127
C00004 -0.195827259
C00006 -0.060922113
C00008 -0.149808082
C00009 0.026376618
C00010 -0.13299999",
"rno","met","kegg")
# Finding connections
dataSet <- QueryNet(dataSet, "met", "kegg", "protein")
dataSet <- QueryNet(dataSet, "met", "kegg", "met")
When I get to the ‘QueryNet’ stage, an error is returned that the webpage cannot be found:
R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(OmicsNetR)
OmicsNetR 1.0.0 initialized Successfully !
> rm(list = ls()) # Clear .GlobalEnv of your R session
>
> # Initiate dataset object. Always do this beforehand
> dataSet <- Init.Data()
A dataset has been initiated.
>
> # Reading in data to be integrated
> prot <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Prot.txt", sep = "\t", header = F)
> met <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Met.txt", sep = "\t", header = F)
>
> dataSet <- PrepareInputList(dataSet,
+ prot,
+ "rno",
+ "protein",
+ "uniprot")
Error in strsplit(geneIDs, "\r|\n|\r\n") : non-character argument
> ?PrepareInputList
> View(prot)
> library(OmicsNetR)
> rm(list = ls()) # Clear .GlobalEnv of your R session
>
> # Initiate dataset object. Always do this beforehand
> dataSet <- Init.Data()
A dataset has been initiated.
>
> # Reading in data to be integrated
> prot <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Prot.txt", sep = "\t", header = F, stringsAsFactors = F)
> met <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Met.txt", sep = "\t", header = F, stringsAsFactors = F)
>
> dataSet <- PrepareInputList(dataSet,
+ prot,
+ "rno",
+ "protein",
+ "uniprot")
Error in strsplit(geneIDs, "\r|\n|\r\n") : non-character argument
> ?read.delim
> a <- "#Entrez logFC
+ 4495 61.12
+ 4496 51.06
+ 4499 23.79
+ 6354 21.04
+ 6369 19.76"
>
> library(tidyverse)
── Attaching core tidyverse packages ────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.2 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.3 ✔ tibble 3.2.1
✔ lubridate 1.9.2 ✔ tidyr 1.3.0
✔ purrr 1.0.2
── Conflicts ──────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package to force all conflicts to become errors
> ?format_delim
> a <- format_delim(prot, delim = "\t", na = "NA", appened = F, col_names = F)
Error in format_delim(prot, delim = "\t", na = "NA", appened = F, col_names = F) :
unused argument (appened = F)
> a <- format_delim(prot, delim = "\t", na = "NA", append = F, col_names = F)
> b <- "#Entrez logFC
+ 4495 61.12
+ 4496 51.06
+ 4499 23.79
+ 6354 21.04
+ 6369 19.76"
> a <- format_delim(prot, delim = "\", na = "NA", append = F, col_names = F)
Error: unexpected numeric constant in "a <- format_delim(prot, delim = "\", na = "NA"
> a <- format_delim(prot, delim = "\n", na = "NA", append = F, col_names = F)
> a <- format_delim(prot, delim = "\n", na = "NA", append = F, col_names = T)
> a <- format_delim(prot, delim = "\n", na = "NA", append = F, col_names = F)
> a <- format_delim(prot, delim = " ", na = "NA", append = F, col_names = F)
Restarting R session...
> library(OmicsNetR)
OmicsNetR 1.0.0 initialized Successfully !
> rm(list = ls()) # Clear .GlobalEnv of your R session
>
> # Initiate dataset object. Always do this beforehand
> dataSet <- Init.Data()
A dataset has been initiated.
>
> # Reading in data to be integrated
> prot <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Prot.txt", sep = "\t", header = F)
> prot <- format_delim(prot, delim = " ", na = "NA", appened = F, col_names = F)
Error in format_delim(prot, delim = " ", na = "NA", appened = F, col_names = F) :
could not find function "format_delim"
Restarting R session...
> library(tidyverse)
── Attaching core tidyverse packages ────────────────────────────────────────────────── tidyverse 2.0.0 ──
✔ dplyr 1.1.2 ✔ readr 2.1.4
✔ forcats 1.0.0 ✔ stringr 1.5.0
✔ ggplot2 3.4.3 ✔ tibble 3.2.1
✔ lubridate 1.9.2 ✔ tidyr 1.3.0
✔ purrr 1.0.2
── Conflicts ──────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()
ℹ Use the conflicted package to force all conflicts to become errors
> library(OmicsNetR)
OmicsNetR 1.0.0 initialized Successfully !
> rm(list = ls()) # Clear .GlobalEnv of your R session
>
> # Initiate dataset object. Always do this beforehand
> dataSet <- Init.Data()
A dataset has been initiated.
>
> # Reading in data to be integrated
> prot <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Prot.txt", sep = "\t", header = F)
> prot <- format_delim(prot, delim = " ", na = "NA", appened = F, col_names = F)
Error in format_delim(prot, delim = " ", na = "NA", appened = F, col_names = F) :
unused argument (appened = F)
> library(tidyverse)
> library(OmicsNetR)
> rm(list = ls()) # Clear .GlobalEnv of your R session
>
> # Initiate dataset object. Always do this beforehand
> dataSet <- Init.Data()
A dataset has been initiated.
>
> # Reading in data to be integrated
> prot <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Prot.txt", sep = "\t", header = F)
> prot <- format_delim(prot, delim = " ", na = "NA", append = F, col_names = F)
>
> met <- read.csv("OmicsNet and OmicsAnalyst Files/OmicsNet_Met.txt", sep = "\t", header = F)
> met <- format_delim(met, delim = " ", na = "NA", append = F, col_names = F)
>
> dataSet <- PrepareInputList(dataSet, prot, "rno", "protein", "uniprot")
trying URL 'https://www.omicsnet.ca/OmicsNet/resources/data/rno/entrez_uniprot.rds'
Content type 'unknown' length 82917 bytes (80 KB)
downloaded 80 KB
Preparing input list with the type of protein completed.
>
> dataSet <- PrepareInputList(dataSet, met, "rno","met","kegg")
trying URL 'https://www.omicsnet.ca/OmicsNet/resources/data/lib/compound_db.rds'
Content type 'unknown' length 671698 bytes (655 KB)
downloaded 655 KB
Preparing input list with the type of met completed.
> # Finding connections
> dataSet <- QueryNet(dataSet, "met", "kegg", "protein")
protein met kegg TRUE 900 inverse FALSE FALSE
Loading required package: RJSONIO
Loading required package: RSQLite
trying URL 'https://www.xialab.ca/resources/sqlite/omicsnet_met.sqlite'
Error in download.file(DonwloadLink, sqlite_Path) :
cannot open URL 'https://www.xialab.ca/resources/sqlite/omicsnet_met.sqlite'
In addition: Warning messages:
1: In download.file(DonwloadLink, sqlite_Path) :
downloaded length 0 != reported length 0
2: In download.file(DonwloadLink, sqlite_Path) :
cannot open URL 'https://www.xialab.ca/resources/sqlite/omicsnet_met.sqlite': HTTP status was '404 Not Found'
I have also tired running the example date here; OmicsNet (specifically case 2) and a similar error is returned:
# Step 2. Map list of miRNA to the application
> dataSet<-PrepareInputList(dataSet,
+ "hsa-mir-101-3p
+ hsa-mir-133b
+ hsa-mir-147a
+ hsa-mir-3140-3p
+ hsa-mir-361-5p
+ hsa-mir-510-5p", "hsa", "mir", "mir_id");
trying URL 'https://www.xialab.ca/resources/sqlite/mir2gene.sqlite'
Error in download.file(DonwloadLink, sqlite_Path) :
cannot open URL 'https://www.xialab.ca/resources/sqlite/mir2gene.sqlite'
In addition: Warning messages:
1: In download.file(DonwloadLink, sqlite_Path) :
downloaded length 0 != reported length 0
2: In download.file(DonwloadLink, sqlite_Path) :
cannot open URL 'https://www.xialab.ca/resources/sqlite/mir2gene.sqlite': HTTP status was '404 Not Found'
Is there any way that I can access the page?
Thanks.
Session Info:
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.utf8 LC_CTYPE=English_Australia.utf8
[3] LC_MONETARY=English_Australia.utf8 LC_NUMERIC=C
[5] LC_TIME=English_Australia.utf8
time zone: Australia/Sydney
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RSQLite_2.3.1 RJSONIO_1.3-1.8 OmicsNetR_1.0.0 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[7] dplyr_1.1.2 purrr_1.0.2 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.3
[13] tidyverse_2.0.0
loaded via a namespace (and not attached):
[1] bit_4.0.5 gtable_0.3.4 crayon_1.5.2 compiler_4.3.1 tidyselect_1.2.0
[6] Rcpp_1.0.11 blob_1.2.4 parallel_4.3.1 scales_1.2.1 fastmap_1.1.1
[11] R6_2.5.1 generics_0.1.3 Cairo_1.6-1 munsell_0.5.0 DBI_1.1.3
[16] pillar_1.9.0 tzdb_0.4.0 rlang_1.1.1 utf8_1.2.3 cachem_1.0.8
[21] stringi_1.7.12 bit64_4.0.5 memoise_2.0.1 timechange_0.2.0 cli_3.6.1
[26] withr_2.5.0 magrittr_2.0.3 grid_4.3.1 vroom_1.6.3 rstudioapi_0.15.0
[31] hms_1.1.3 lifecycle_1.0.3 vctrs_0.6.3 glue_1.6.2 fansi_1.0.4
[36] colorspace_2.1-0 tools_4.3.1 pkgconfig_2.0.3