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.
Related
I have merged two data sets (data1.csv and data2.csv) and created a data file to run the analyses on. But, when I do the analysis, R cannot recognize some of my columns (variables). My analysis is a multinational logit one.
The code for analysis is:
library(nnet)
mlogit<- multinom(groupadmit~mid_pop, tot_male10, tot_female10, male16,
tot_female16, agemean10, agemean16, IMD_score, IMD_score2, data =
admitqof10_16)
and the error is:
Error in model.frame.default(formula = groupadmit ~ mid_pop, data =
admitqof10_16, :
object 'male16' not found
I tried a couple of ways to solve the problem. For example, I use ls() to see whether the created data.table is in the R or not and it was there. I changed the name of the variable, but again it does not work. I exported the created data and imported it again. But, I have failed.
May someone please help me know why this problem happens and what I can do to resolve it?
Thanks in advance
I am trying to create a script that I run about once a week. The goal is that it will go out and check an MS Excel file that a co-worker manages. It then tests to see if the date the file was modified is newer then the last time it was imported. If it is newer, it will import the file (I am using readxl package - WONDERFUL!) into a new object that is a named with the date the original Excel file was last modified included in the object name. I have everything working except for the assignment of the imported data.frame to a new object that includes the date.
An example of the code I am using is:
First I create an object with a path pointing to the file of interest.
pfdFilePath <- file.path("H:", "3700", "3780", "002-00", "3.
Project Information", "Program", "RAH program.xls")
after testing to verify the file has been modified, I have tried simple assignment ("test" is just an example for simplification):
paste("df-", as.Date(file.info(pfdFilePath)$mtime), sep = "") <- "test"
But that code produces an error:
Error in paste("df-", as.Date(file.info(pfdFilePath)$mtime), sep = "") <- "test" :
target of assignment expands to non-language object
I then try the assign function:
assign(paste("df-", as.Date(file.info(pfdFilePath)$mtime), sep = ""), "test")
Running this code creates an object that looks to be okay, but when I evaluate it, or try using str() or class() I get the following error:
Error in df - df-2016-08-09 :
non-numeric argument to binary operator
I am pretty sure this is an error that has to do with the environment I am using assign, but being relatively new to R, I cannot figure it out. I understand that the assign function seems to be frowned upon, but those warnings seem to centered on for-loops vs. lapply functions. I am not really iterating within a function though. Just a dynamically named object whenever I run a script. I can't come up with a better way to do it. If there is another way to do this that doesn't require the assign function, or a better way to use assign function , I would love to know it.
Thank you in advance, and sorry if this is a duplicate. I have spent the entire evening digging and can't derive what I need.
Abdou provided the key.
assign(paste0("df.", "pfd.", strftime(file.info(pfdFilePath)$mtime, "%Y%m%d")), "test01")
I also converted to the cleaner paste0 function and got rid of the dashes to avoid confusion. Lesson learned.
Works perfectly.
I am trying to prepare data for cluster analysis. That's why I have prepared data tables in excel and the headers are "id","name","crime_type","crime_date","gender","age"
Then , I convert the excel into .csv format.
Then , I write the following command ->
>crime <- read.csv("crime_data.csv",header=T)
>crime # I print , and it prints
# now I will do cluster with kmeans()
>kmeans.result <- kmeans(crime,3)
But , it shows errors.
"Error is as follows :
Error in do_one(nmeth) : NA/NaN/Inf in foreign function call (arg 1)
In addition: Warning message:
In kmeans(crime, 3) : NAs introduced by coercion"
What I am doing wrong here...
I can't speak to your specific problem without knowing what you data looks like but it could be as simple as giving the xlsx package a try. I think it handles NaNs better
install.packages(xlsx)
library(xlsx)
yourdata <- read.xlsx("YOURDATASHEET.xlsx", sheetName="THESHEETNAME")
Seems like you are asking two questions. For the first; you can also try reading directly from the clipboard (beware of large tables tough, but so far I have good results with 40k rows, 30 col)
d1<-read.table(file="clipboard",sep="\t",header=FALSE,stringsAsFactors=FALSE)
set header to TRUE if you want to name your columns. You can also use what was suggested above to open excel sheets directly but this might not be practical if you have non standard tables.
For the second part perhaps you should convert to numerical using the sapply function and or suppressWarnings().
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 doing following in Cooccur library in R.
> fb<-read.table("Fb6_peaks.bed")
> f1<-read.table("F16_peaks.bed")
everything is ok with the first two commands and I can also display the data:
> fb
> f1
But when I give the next command as given below
> explore_pairs(c("fb", "f1"))
I get an error message:
Error in sum(sapply(tf1_s, score_sample, tf2_hits = tf2_s, hit_list = hit_l)) :
invalid 'type' (list) of argument
Could anyone suggest something?
Despite promising to release a version to the Bioconductor depository in the article the authors published over a year ago, they have still not delivered. The gz file that is attached to the article is not of a form that my installation recognizes. Your really should be corresponding with the authors for this question.
The nature of the error message suggests that the function is expecting a different data class. You should be looking at the specification for the arguments in the help(explore_pairs) file. If it is expecting 2 matrices, then wrapping data.matrix around the arguments may solve the problem, but if it is expecting a class created by one of that packages functions then you need to take the necessary step to construct the right objects.
The help file for explore_pairs does exist (at least in the MAN directory) and says the first argument should be a character vector with further provisos:
\arguments{
\item{factornames}{an vector of character strings, each naming a GFF-like
data frame containing the binding profile of a DNA-binding factor.
There is also a load utility, load_GFF, which I assume is designed for creation of such files.
Try rename your data frame:
names(fb)=c("seq","start","end")
Check the example datasets. The column names are as above. I set the names and it worked.