Currently I am trying to understand DEXSeq package. I have a design tsv file and 7 files which contains Counts. Now would like to run the following command
library("DEXSeq");
design=read.table("dexseq_design.tsv", header=TRUE, row.names=1);
ecs = DEXSeqDataSetFromHTSeq(countfiles=c("M0.txt", "M1.txt", "M2.txt", "M3.txt", "M4.txt", "M5.txt", "M6.txt", "M7.txt"), design=design, flattenedfile="genome.chr.gff");
The last command gives and error
Error in class(sampleData) %in% c("data.frame") :
error in evaluating the argument 'x' in selecting a method for function '%in%':
Error: argument "sampleData" is missing, with no default
What does this error means and how to fix it? While loading the package DEXSeq there was a warning
Warning message:
replacing previous import by ‘ggplot2::Position’ when loading ‘DESeq2’
Related
I have been getting this error for the first time for commands that used to run well before:
# conversion from char to numeric:
as.numeric(df$col) -> df$col
Error: (converted from warning) NAs introduced by coercion
# running metafor
rma(yi, vi, data=r1s2)
Error: (converted from warning) Studies with NAs omitted from model fitting.
The issue must be with the R environment as these commands are running perfectly on a different computer. The only wrong I can think of is installing a package from GitHub or updating R a few hours ago. The only relevant answer I've found so far is also not working:
Sys.setenv(R_REMOTES_NO_ERRORS_FROM_WARNINGS="true")
This seems to be a warning level issue. If the warning level is 2, warnings become errors. From the documentation, my emphasis.
warn:
integer value to set the handling of warning messages. If warn is negative all warnings are ignored. If warn is zero (the default) warnings are stored until the top–level function returns. If 10 or fewer warnings were signalled they will be printed otherwise a message saying how many were signalled. An object called last.warning is created and can be printed through the function warnings. If warn is one, warnings are printed as they occur. If warn is two (or larger, coercible to integer), all warnings are turned into errors.
old_ops <- options(warn = 2)
warning("this is a warning")
#> Error in eval(expr, envir, enclos): (converted from warning) this is a warning
x <- "a"
as.numeric(x)
#> Error in eval(expr, envir, enclos): (converted from warning) NAs introduced by coercion
options(old_ops)
Created on 2022-06-25 by the reprex package (v2.0.1)
If you say that
The issue must be with the R environment as these commands are running perfectly on a different computer.
then check if you have a file named .RData in your R startup directory. If you have one, then you probably set the warning level in a previous session and now it is being restored every time you run R. Delete this file and this behavior will go away.
See also this SO post.
I'm trying to use {reticulate} to load in a .pkl file. So far I've just loaded the package and tried to import pandas, i.e.:
library(reticulate)
pd<-import("pandas")
For some reason I'm getting this error, but can't make any sense of it:
Error: invalid version specification ''/home'', '..EXE was started with the above path as the current directory.', '. paths are not supported. Defaulting to Windows directory.'
In addition: Warning message:
In if (grepl("\\.$", v)) v <- paste0(v, "9000") :
the condition has length > 1 and only the first element will be used
Any tips?
Keep getting the following warning:
"Warning message:
In data(VEMCOdata) : data set ‘VEMCOdata’ not found"
I'm new to R. I set up all my files exactly how the package VTrack specified. I set my working directory, load my first data set then ue the command >data(xx) and keep getting the same warning message.
setwd("C:/Users/gwhite/Desktop")
library(VTrack)
VEMCOdata <- read.csv('VEMCOdata_2014.csv')
data(VEMCOdata)
Warning message:
In data(VEMCOdata) : data set ‘VEMCOdata’ not found
I'm trying to use root from the ape package in R, but I keep getting the following error:
Error in FUN(X[[i]], ...) : object 'fuseRoot' not found
Here is the code that isn't working:
mammal.trees <- lapply(mammal.trees, root, "Gal", resolve.root=TRUE)
I'm stumped because the same code works for another multiPhylo object just fine.
Trying to use the latest version of methylSig package (0.3.2), and getting an error when using the methylSigCalc function.
I get a cryptic error message after it figures out the number of loci:
Total number of bases: 2.59m
Error in result[, 3] : subscript out of bounds”
I tried running the code of the methylSigCalc function line by line, and the first error I encounter is when it gets to the methylSig_dataProcess function (below is the error after specifying just one core to try to get a useful error message):
Error in do.call(rbind, lapply(which(validLoci),
methylSig_dataProcess, : error in evaluating the argument 'args' in
selecting a method for function 'do.call': Error in match.fun(FUN) :
object 'methylSig_dataProcess' not found
It does seem that methylSig_dataProcess is now missing from the package.
Any suggestions on where I might be going wrong?
Many thanks,
gogatea