I tried to run my code like I usually do, and I got an "unused argument" error message. I have previously run the code multiple times and everything worked perfectly fine, this is the first time I have gotten an error message (I haven't changed the code). The only thing I've done different is I cleared the workspace at the end of my previous session (though I have no idea if this would actually affect it?).
Below is the code:
pacman::p_load(
rio, # importing data
here, # relative file pathways
janitor, # data cleaning and tables
lubridate, # working with dates
epikit, # age_categories() function
tidyverse, # data management and visualization
skimr,
psych,
reshape2, #for reshaping dataset
dplyr,
miscFuncs,
foreign, #read data formats
rcompanion, # group means
eeptools,
plyr)
mesh_dat <- import(here("R", "BTmeshdata.xlsx"))
The error message:
Error in here("R", "BTmeshdata.xlsx") :
unused argument ("BTmeshdata.xlsx")
The issue seems to be in how the dataset is imported because I have the same issue with importing a dataset from a different project.
.here and my folder "R" are located in my Documents folder.
Thanks!
Related
So I use SGA tools for processing my images. It gives back results in .dat files. Now in order to work on this data in R, I tried to import the .dat file using the haven package. I installed haven and then its library, but I am not able to import data still and it gives this error message.
Error: Failed to parse C:/Users/QuRana/Desktop/SGA Tools/Plate_Image_Example (1).dat: This version of the file format is not supported.
When I use this command install.packages("haven"), haven is loaded, but then when I load library using library(haven) nothing appears on my console except for this
> library(haven)
Then when I use this code:
datatrial1 <- read_dta("C:/Users/QuRana/Desktop/SGA Tools/Plate_Image_Example (1).dat")
It gives me the error mentioned above. When I try converting my .dat file to a .csv file and load my data, the imported data adds additional "t" values before the values in columns except for the first one like this:
Flags: S - Colony spill or edge interference C - Low colony circularity
# row\tcol\tsize\tcircularity\tflags
1\t1\t4355\t0.9053\t
1\t2\t4456\t0.8401\t
1\t3\t3439\t0.8219\t
1\t4\t3215\t0.8707\t
All the t's before the numeric values are not what I want. Another issue that I am facing is I cannot install the gitter package on my R version which is R 4.2.2.
You can read your tab separated file like so `read.delim("file_path", header = TRUE, sep = "\t")
I'm getting an error when running getOptionChain from quantmod package.
The code should get Option chain data and subset into a new list that contains only the puts.
The error I get is: Error in .Date(Exp/86400) : could not find function ".Date"
Same code, sometimes runs without error. If I shorten the list of Symbols, there's no error, but the error as far as I know is not related to a specific symbol, because I made to run successfully. Seems random but frequent error.
All symbols are weekly expirations and the desired output is the next weekly expiration, so from my understanding, there's no need to specify a exp date.
library(quantmod)
library(xts)
Symbols<-c ("AA","AAL","AAOI","AAPL","ABBV","ABC","ABNB","ABT","ACAD","ACB","ACN","ADBE","ADI","ADM","ADP",
"ADSK","AEO","AFL","AFRM","AG","AGNC","AHT","AIG","AKAM","ALGN","AMAT","AMBA","AMC","AMD","AMGN",
"AMPX","AMRN","AMRS","AMZN","ANET","ANF","ANY","APA","APO","APPH","APPS","APRN","APT","AR","ARVL")
Options.20221118 <- lapply(Symbols, getOptionChain)
names(Options.20221118) <- Symbols
only_puts_list <- lapply(Options.20221118, function(x) x$puts)
After upgrading to R 4.2.2 the issue is fixed.
We have always been an SPSS shop but we're trying to learn R. Been doing some basics. I am trying to do a simple t-test, just to learn that code.
Here's my code, and what's happening:
Code screenshot
I don't get why it says "score" isn't found. It's in the table, and the read.csv code defaults to assuming the first row contains headers. I can't see why it's not "finding" the column for score. I'm sure it's something simple, but would appreciate any help.
You didn't store your imported csv file in a variable. It printed to the console because it had nowhere else to go - it just gets printed and then thrown away. You need to assign it for it to be saved in memory:
my_data_frame <- read.csv("ttest.csv")
Now your data exists in the variable my_data_frame and you can use it by supplying it as the data argument:
t.test(score ~ class, mu=0, alt="two.sided", conf=0.95, var.eg=F, paired=F, data=my_data_frame)
Also, in general, I would recommend using read_csv from the package readr over the default read.csv - it's faster.
Finally, when you ask questions, please provide your code as text, not a picture. You should also provide your data or a toy dataset - you can use the function dput to print code that will create your data, or just provide the csv file or some code that creates toy data.
I've searched the web for this without much luck. More or less you always get to the example from the VariantAnnotation Package. And since this example works fine on my computer I have no idea why the VCF I created does not.
The problem: I want to determine the number and location of SNPs in selected genes. I have a large VCF file (over 5GB) that has info on all SNPs on all chromosomes for several mice strains. Obviously my computer freezes if I try to do anything on the whole genome scale, so I first determined genomic locations of genes of interest on chromosome 1. I then used the VariantAnnotation Package to get only the data relating to my genes of interest out of the VCF file:
library(VariantAnnotation)
param<-ScanVcfParam(
info=c("AC1","AF1","DP","DP4","INDEL","MDV","MQ","MSD","PV0","PV1","PV2","PV3","PV4","QD"),
geno=c("DP","GL","GQ","GT","PL","SP","FI"),
samples=strain,
fixed="FILTER",
which=gnrng
)
The code above is taken out of a function I wrote which takes strain as an argument. gnrng refers to a GRanges object containing genomic locations of my genes of interest.
vcf<-readVcf(file, "mm10",param)
This works fine and I get my vcf (dim: 21783 1) but when I try to save it won't work
file.vcf<-tempfile()
writeVcf(vcf, file.vcf)
Error in .pasteCollapse(ALT, ",") : 'x' must be a CharacterList
I even tried in parallel, doing the example from the package first and then substituting for my VCF file:
#This is the example:
out1.vcf<-tempfile()
in1<-readVcf(fl,"hg19")
writeVcf(in1,out1.vcf)
This works just fine, but if I only substitute in1 for my vcf I get the same error.
I hope I made myself clear... And any help will be greatly appreciated!! Thanks in advance!
Thanks for reporting this bug. The problem is fixed in version 1.9.47 (devel branch). The fix will be available in the release branch after April 14.
The problem was that you selectively imported 'FILTER' from the 'fixed' field but not 'ALT'. writeVcf() was throwing an error because there was no ALT value to write out. If you don't have access to the version with the fix, a work around would be to import the ALT field.
ScanVcfParam(fixed = c("ALT", "FILTER"))
You can see what values were imorted with the fixed() accessor:
fixed(vcf)
Please report and bugs or problems on the Bioconductor mailing list Martin referenced. More Bioc users will see the question and you'll get help more quickly.
Valerie
Here's a reproducible example
library(VariantAnnotation)
fl <- system.file("extdata", "chr22.vcf.gz", package="VariantAnnotation")
param <- ScanVcfParam(fixed="FILTER")
writeVcf(readVcf(fl, "hg19", param=param), tempfile())
## Error in .pasteCollapse(ALT, ",") : 'x' must be a CharacterList
The problem seems to be that writeVcf expects the object to have an 'ALT' field, so
param <- ScanVcfParam(fixed="ALT")
writeVcf(readVcf(fl, "hg19", param=param), tempfile())
succeeds.
I am trying to use bin() on my big data set. I am using the Lahman data set as an example: http://www.seanlahman.com/baseball-archive/statistics/
I am using the comma-delimited version and looking at the 'Batting' csv file. My data set will be much, much bigger, but if my program cannot handle this, it can't handle my bigger data set.
This is what I am trying to do currently:
> require(devtools)
> require(bigvis)
> bigData <- read.csv("GCdataViz/lahman2012-csv/Batting.csv")
> bigDataNum <- bigData[,sapply(bigData,is.numeric)]
> bin(bigDataNum)
Error: is.numeric(x) is not TRUE
I first got an error when I tried to use bin() because my data set wasn't all numeric. So I used sapply() with the is.numeric parameter, but still got the error that my data set wasn't numeric.
The bigvis library doesn't have much documentation. Should I smooth() after the condense method or go ahead and autoplot(). Is there anyway I can specify plots like bar graphs, line graphs, box, etc?
EDIT: my error: