FraserDataSet() error in FRASER
Hello, I'm trying to use FRASER package for splicing events. So far, I created these files;
data_dir <- "/home/user/rnaseq/data" junctions <- fread(file.path(data_dir, "junction_counts.tsv"), header=TRUE) splicesite <- fread(file.path(data_dir, "splicesite_counts.tsv"), header=TRUE) coldata <- fread(file.path(data_dir, "exp_design_fraser.tsv"), header=TRUE)
> head(junctions)
seqnames start end width strand startID endID 3618-A 3618-B 3619-A
<char> <int> <int> <int> <char> <int> <int> <int> <int> <int>
1: GL000009.2 56679 83041 26362 - 233135 242663 0 0 1
2: GL000194.1 112851 114985 2134 - 233137 242664 0 12 16
3: GL000194.1 156538 163935 7397 + 233138 242665 0 0 2
4: GL000194.1 49195 55487 6292 + 233139 242670 0 0 0
5: GL000194.1 52037 55487 3450 + 233140 242670 0 0 0
6: GL000194.1 53863 54677 814 - 233141 242666 0 0 0
3619-B 3620-A 3620-B
<int> <int> <int>
1: 0 0 0
2: 10 51 24
3: 0 0 0
4: 0 5 0
5: 0 5 0
6: 0 0 3
> head(splicesite)
seqnames start end width strand spliceSiteID type 3618-A 3618-B 3619-A
<char> <int> <int> <int> <char> <int> <char> <int> <int> <int>
1: chr1 12722 13482 1 + 1 Acceptor 0 0 0
2: chr1 14615 16857 2 + 2 Donor 0 0 0
3: chr1 14738 14969 2 + 3 Donor 0 0 0
4: chr1 14788 16875 2 + 4 Donor 0 0 0
5: chr1 14830 14929 2 + 5 Donor 0 0 0
6: chr1 14830 14969 2 + 6 Donor 0 0 0
3619-B 3620-A 3620-B
<int> <int> <int>
1: 0 0 0
2: 0 0 0
3: 0 0 0
4: 0 0 0
5: 0 0 0
6: 0 0 0
and I checked the files;
> dim(junctions)
[1] 339402 13
> dim(splicesite)
[1] 1111024 13
When I tried creating FRASER object, an error occured:
fds <- FraserDataSet(
workingDir = data_dir,
junctions = junctions,
spliceSites = splicesite,
colData = coldata
)
Error in SummarizedExperiment(rowRanges = junctions[, c("startID", "endID")], :
the rownames and colnames of the supplied assay(s) must be NULL or
identical to those of the RangedSummarizedExperiment object (or
derivative) to construct
How to solve it? Thank you.
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Hi, the solution still seems to suggest the same error. Since the rownames of junctions need to be derived from "startID" and "endID" so that they match the rowRanges required by Fraser, you have two options:
1) Remove the rownames from both:
2) Standardize the rownames so that they match those expected:
I don't know which one is the best solution; try them separately and see if it creates the FRASER object.
Let me know,
Regards,
Marco
Thank you for reply. When I run the first option, nothing's changed, same error occured. However, in second option this error occured;
Not having full insight into the structure of a FRASER object, I wrote the code I thought might work. You can try making the rownames unique:
Thanks but still encounter the same problem;
Error in SummarizedExperiment(rowRanges = junctions[, c("startID", "endID")], : the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the RangedSummarizedExperiment object (or derivative) to construct
Can you show the
colDatadata? It’s important thatcolData$sampleIDis identical torownames(colData)and to the sample names injunctionsandspliceSites.It looks like that;