tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
2
0
Entering edit mode
@3279cb16
Last seen 12 weeks ago
United States

Hello, I am having an error running DESeq2 (specifically on the DESeqDataSetFromTximport step) after pseudo-aligning my transcriptomic data with Kallisto. I got the code below from this source: UT Austin Wiki

R

#load libraries
library(tximport)
library("DESeq2")


#Import a file called file_list with all the locations of the abundance.tsv files
#eg below:
#/stor/SCRATCH/sample1/abundances.tsv
#/stor/SCRATCH/sample2/abundances.tsv
#/stor/SCRATCH/sample3/abundances.tsv
#/stor/SCRATCH/sample4/abundances.tsv
files<-as.character(read.table("path/to/file_list.txt", header=FALSE)$V1)
#Import a file called samples with the sample names corresponding to each file in the file_list
#eg below:
#sample1
#sample2
#sample3
#sample4
#look at the data structures
files
#OUTPUT: 
#[1] "/path/to/BMRNA2_sulcia_kallisto/abundance.tsv"    
#[2] "/path/to/BMRNA4_sulcia_kallisto/abundance.tsv"    
#I truncated this because I have 50 samples total
#[50] "/path/to/BMRNANo14_sulcia_kallisto/abundance.tsv"

samples<-as.character(read.table("/path/to/samples.txt",header=FALSE)$V1)
names(files)<-samples
#look at the data structures
samples
#OUTPUT: 
#[1] "BMRNA2_sulcia_kallisto"     "BMRNA4_sulcia_kallisto" 
#truncated again...
#[49] "BMRNANo13c_sulcia_kallisto" "BMRNANo14_sulcia_kallisto"
files
#OUTPUT:
#BMRNA2_sulcia_kallisto 
#   "/Users/mckinleesalazar/Desktop/Dis_stuff/Data/sulcia_transcript/sulcia/just_tsv/BMRNA2_sulcia_kallisto/abundance.tsv"

#Import a file called sampletable which is a tab-delimited file that contains each samplename along with the condition
#eg below:
#samples        condition
#sample1        alc
#sample2        alc
#sample3        con
#sample4        con
sampleTable <-read.table("/path/to/sampletable.txt",header=TRUE, row.names=1)
#look at the data structure
head(sampleTable)
#OUTPUT: 
#Condition
#BMRNA2_sulcia_kallisto   Control1
#BMRNA4_sulcia_kallisto   Control2
#BMRNA12_sulcia_kallisto  Control3
#BMRNA13_sulcia_kallisto  Control4
#BMRNA14_sulcia_kallisto  Control5
#BMRNA20_sulcia_kallisto  Control6


#IMPORTANT: MAKE SURE THE SAMPLES AND FILE_LIST ARE IN THE SAME ORDER- SAMPLES SHOULD MATCH UP WITH FILES
samples==rownames(sampleTable) #should return TRUE for all
#OUTPUT: 
#[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#[19] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
#[37] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE


#Import a file called tx2gene.csv which a csv file that contains the transcript id to gene id mapping
#For Drosophila, this is located at: tx2gene.csv
tx2gene <- read.csv("/path/to/tx2gene.csv")

#Sample of what the .csv format 
#TXNAME,GENEID
#SULC_00001,50S ribosomal protein L35
#SULC_00002,Chaperone protein DnaK
#SULC_00003,50S ribosomal protein L13
#SULC_00004,30S ribosomal protein S9
#SULC_00005,30S ribosomal protein S2
#SULC_00006,tRNA-Leu(taa)
#SULC_00007,tRNA-Gly(gcc)

#look at this data structure
#read in kallisto abundance files, summarizing by gene
txi <- tximport(files, type = "kallisto", tx2gene = tx2gene)
names(txi)
#OUTPUT: 
#[1] "abundance"           "counts"              "length"              "countsFromAbundance"


#make a deseq2 object from the kallisto summarized counts
ddsMatrix <- DESeqDataSetFromTximport(countData = txi, colData = sampleTable, design = ~Condition)
ddsMatrix
#OUTPUT ERROR MESSAGE: 
#Error in is(txi, "list") : argument "txi" is missing, with no default

I am not very experienced in R, but is the issue with the txi data table? I have included a screenshot of what it looks like when I view it in R studios. Is this the correct format? I.e., Should all the counts data be in a single column/row like it appears in the viewer? This doesn't seem right to be given the line:

DESeqDataSetFromTximport(countData = txi, colData = sampleTable, design = ~Condition)

It looks like it is finding the column data from 'sampleTable' but is not able to find the count data from txi. This is why I think it is a format issues in 'txi', but I cannot find an example of the expected format for the txi table.

screenshot of txi format

I would appreciate any help/guidance from an experienced R user. Thanks, McKinlee

tximport DESeq2 • 446 views
ADD COMMENT
2
Entering edit mode
@mikelove
Last seen 10 hours ago
United States

argument txi is missing, with no default

This means the function was expecting a named argument txi

Check the man page for the function:

?functionName

You can see a usage example that way

ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 10 hours ago
United States

The arguments for that function can be found in the help page (accessed using ?DESeqDataSetFromTximport)

Usage:

     DESeqDataSet(se, design, ignoreRank = FALSE)

     DESeqDataSetFromMatrix(
       countData,
       colData,
       design,
       tidy = FALSE,
       ignoreRank = FALSE,
       ...
     )

     DESeqDataSetFromHTSeqCount(
       sampleTable,
       directory = ".",
       design,
       ignoreRank = FALSE,
       ...
     )

     DESeqDataSetFromTximport(txi, colData, design, ...)

And you can see that there is no argument called 'countData', but there is one called 'txi'. You need to change your function call to use 'txi = txi' instead of 'countData = txi'.

Login before adding your answer.

Traffic: 405 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6