I'm running the following code in r and it is not working. getBM seems to not work for any arguments. Am I doing something wrong?
ibrary(biomaRt)
ensembl <- useEnsembl(biomart = "genes")
ensembl <- useEnsembl(biomart = "ensembl",
dataset = "hsapiens_gene_ensembl",
mirror = "useast")
affyids <- c("202763_at","209310_s_at","207500_at")
getBM(attributes = c('affy_hg_u133_plus_2', 'entrezgene_id'),
filters = 'affy_hg_u133_plus_2',
values = affyids,
mart = ensembl)
The error I'm getting is
Error in getNodeSet(html, path = "//div[#class='plain-box float-right archive-box']")[[1]] : subscript out of bounds
I tried this both in r version 3.6.3 and 4.1
Ensembl is temporarily unavailable according to https://www.ensembl.org/info/.
Related
When trying to use the cSPADE algorithm from the arulesSequences package in R I always receive the following error:
Error in makebin(data, file) : 'sid' invalid (order)
I think the problem is related to the arrangement of the data somehow but I really don't know what the problem may be.
A similar problem was presented here but the solution that I tried to incorporate by using
arrange(sessions#itemsetInfo,sequenceID,eventID)
did not change anything. Thanks for your help!
#This is how I pre-processed the data
load("example.Rda")
example.Rda %>% head(5) %>% knitr::kable()
str(example.Rda)
example.Rda = as.data.frame(example.Rda)
sessions <- as(example.Rda %>% transmute(items = question_type), "transactions")
transactionInfo(sessions)$sequenceID <- example.Rda$user_id
transactionInfo(sessions)$eventID <- example.Rda$item_id
itemLabels(sessions) <- str_replace_all(itemLabels(sessions), "items=", "")
inspect(head(sessions,10))
arrange(sessions#itemsetInfo,sequenceID,eventID)
str(sessions)
View(sessions)
#This is the definition of the itemsets after which the error occurs
itemsets <- cspade(sessions,
parameter = list(support = 0.001),
control = list(verbose = FALSE))
I want to parse the AAChange.refGene column and then use biomaRt R package to extract information. My code is raising Error in is.single.string(object) : argument "object" is missing, with no default even though the getSequence function is meant to accept multiple arguments.
library(tidyr)
variant_calls = read.delim("variant_calls.txt")
info = tidyr::separate(variant_calls["AAChange.refGene"], AAChange.refGene, c("Refseq ID", "cDNA level change", "Protein level change"), ":")
df = cbind(variant_calls["Gene.refGene"],info)
library(biomaRt)
ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="https://grch37.ensembl.org", path="/biomart/martservice")
pep <- vector()
for(i in 1:length(df$`Refseq ID`)){
temp <- getSequence(id=df$`Refseq ID`[i],type='refseq_mrna',seqType='peptide', mart=ensembl)
temp <- sapply(temp$peptide, nchar)
temp <- sort(temp, decreasing = TRUE)
temp <- names(temp[1])
pep[i] <- temp
}
df$Sequence <- pep
Traceback:
Error in is.single.string(object) :
argument "object" is missing, with no default
I got the same error and found out (using ?getSequence) that it was a conflict between packages (classic R), specifically biomart and seqinr which is used to handle fasta format thus probably used together often.
My solution consisted in calling the function like this:
biomaRt::getSequence()
I use the latest version of package and I try to run this:
I try to run this example:
library(bibliometrix)
download.file("https://www.bibliometrix.org/datasets/joi.zip", destfile = temp<-tempfile())
M <- convert2df(readLines(unz(temp, "joi.txt")), dbsource="isi",format="plaintext")
CS <- conceptualStructure(M, method="MCA", field="ID", minDegree=10, clust=5, stemming=FALSE, labelsize=8,documents=20)
but I receive this error:
Error in conceptualStructure(M, method = "MCA", field = "ID", minDegree = 10, :
unused argument (clust = 5)
What should change?
I want to perform basket analysis and draw a paracoord plot however I receive an error.
Content of this error is: :
Error in m[j, i] : subscript out of bounds.In addition: Warning message:
In cbind(pl, pr) :
number of rows of result is not a multiple of vector length (arg 2)
I am using data from: Link.
First I am transforming this to fit basket analysis, name of the original excel files is Online_Retail:
library(arules)
library(arulesViz)
library(plyr)
items <- ddply(Online_Retail, c("CustomerID", "InvoiceDate"), function(df1)paste(df1$Description, collapse = ","))
items1 <- items["V1"]
write.csv(items1, "groceries1.csv", quote=FALSE, row.names = FALSE, col.names = FALSE)
trans1 <- read.transactions("groceries1.csv", format = "basket", sep=",",skip=1)
And to draw paracoord I have created such a code:
rules.trans2<-apriori(data=trans1, parameter=list(supp=0.001,conf = 0.05),
appearance=list(default="rhs", lhs="ROSES REGENCY TEACUP AND SAUCER"), control=list(verbose=F))
sorted.plot <- sort(rules.trans2, by="support", decreasing = TRUE)
plot(sorted.plot, method="paracoord", control=list(reorder=TRUE, verbose = TRUE))
Why my code for paracoord is not working? how can I fix it? What should I change?
This is, unfortunately, a bug in arulesViz. This will be fixed in the next release (arulesViz 1.3-3). The fix is already available in the development version on GitHub: https://github.com/mhahsler/arulesViz
I'm using the DESeq package to analyze RNA sequencing data. I have only one replicate and two treatments. My code is:
data <- read.csv()
metadata <- data.frame(row.names = colnames(data), condition =c("treated", "untreated"))
cds2 <- newCountDataSet( countData = data, conditions = metadata )
cds2 <- estimateSizeFactors(cds2)
counts( cds2, normalized=TRUE )
cds2 <- estimateDispersions(cds2, method="blind", sharingMode="fit-only")
res <- nbinomTest(cds2, "treated", "untreated" )
Everything works fine until I call "estimateDispersions". However, the function "nbinomTest" gives me this error:
Error in if (dispTable(cds)[condA] == "blind" || dispTable(cds)[condB] == :
missing value where TRUE/FALSE needed
I found some documentation on this error, but the answers are not helpful for me. I work with R version 3.1.2 (2014-10-31).
Can someone help my with my problem, please?
Cheers!