Questions tagged [rhdf5]
35 questions
1
vote
0 answers
HDF5 dataspace interface - What does it do and what is it's real world application
I am currently building some applications which make use of HDF5 files. My language of choice is R.
I have already taken a look at the hdfgroup website with regards to dataspace and I think I understand the concept. But I am very much unable to…
FoldedChromatin
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1
vote
1 answer
Selecting pairs of numbers from a dataframe
I have a dataframe like this:
row col
1 1
1 50
1 55
2 75
and I want to select all the row and col values that are paired so I can insert them into a function.
I am trying this code:
library(rhdf5)
for(row in df$row){
for…
Stefano Potter
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1
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0 answers
How can I allocate a DataSet larger than will fit in memory in R?
I have an external application (non-R) whose input is an HDF5 file containing a dense data cube. I wish to generate the data for that in R.
The normal way to create an HDF5 DataSet in R would be like:
`
library(h5)
data <- numeric(…
P.Hays
- 17
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1
vote
1 answer
How do I save variables from hdf5 file using strings as variable names?
I have a hdf5 file with multiple variables that I want to automatically store in a list or a matrix.
library(rhdf5)
file = H5Fopen("myfile.h5")
file
HDF5 FILE
name /
filename
name otype dclass …
Herman Toothrot
- 1,463
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0
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1 answer
why reading group in hdf5 in r throws H5Identifier not valid?
I have downloaded data from archs rnaseq data. The human hdf5 file (28G). I want to access the expression data and group information. I am using the below code:
h5_exprs <- h5read("archs4_gene_human_v2.1.2.h5", "data/expression")
It throws
Error…
Nmgh
- 113
- 7
0
votes
2 answers
Cannot write int16 data type using the R's rhdf5 package
In R I would like to write a matrix of integers into an HDF5 file ".h5" as an int16 data type. To do so I am using the rhdf5 package. The documentation says that you should set one of the supported H5 data types when creating the dataset. However,…
user21816
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- 6
0
votes
1 answer
Why can I open HDF5 files from local disk but not external disk using the rhdf5 R package?
I am having an issue which I came across using the R package "sleuth" to analyze RNAseq data. The problem clearly depends on rhdf5, however. The issue boils down to this error, which I only get when trying to read a .h5 file from my external SSD but…
bkleiboeker
- 21
- 3
0
votes
0 answers
R and rhdf5: Each function throws a Error: segfault from C stack overflow
I installed the rhdf5 package with BiocManager and wanted to use the h5write function to write a dataframe to a hdf5 file. But with each function from this package I only get:
> rhdf5::h5write(df, file="test3.hdf5", name ="table")
Error: segfault…
JcGKitten
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- 3
0
votes
0 answers
How read .hdf5 file with name like (1,1)?
I have an hdf5 file that I would like to read the subgroup of it.
file is 'GSE77565_FBD_IC-heatmap-chr-10k.hdf5.gz' that downloaded from GEO number= 'GSE77565'
I read the data like below:
library(rhdf5)
h5f = H5Fopen("file.hdf5")
h5f
HDF5 FILE
…
star
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0
votes
2 answers
Empty strings writing data with rhdf5
I'm having trouble writing strings to groups in hdf5 files using rhdf5 using the low-level API, and specifically the functions
H5Fcreate
H5Gcreate
H5Screate
H5Dcreate
H5Dwrite
Here's my data:
# strings
v <- c("val1", "val2", "cat", "dog")
I'd…
Mittenchops
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0
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1 answer
Need to read several .h5 files using loop with indices
I have been given a crap ton of files I need to read over and graph. Some of the datasets have more files that other. So I need to write a loop that will do this. The code that I have written so far works but I cannot for the life of me figure out…
alittleloopy
- 63
- 9
0
votes
1 answer
How to fix 'gcc: error: "/usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a": No such file or directory' in R
I am trying to install minfi in R:
BiocManager::install("minfi")
but the installation stops during the compiling of HDF5Array with the following errors:
gcc: error: "/usr/lib64/R/library/Rhdf5lib/lib/libhdf5.a": No such file or
directory
gcc:…
Makis Ladoykakis
- 111
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0
votes
1 answer
Reading .h5 file in R
I have a '.h5' file and want to extract it using R.
I searched and found rhdf5 from BiocManager is used for this purpose. I tried it and I got an error. No matter if I use either 'h5ls' or 'h5read' methods, I always get the same error message…
hcacode
- 75
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0
votes
0 answers
Not a valid jar
I am new to R Programming.
I am using below code after setting all env variables. All connections are working well but I am getting an error in executing below of to.dfs.
Please guide…
user8915561
0
votes
0 answers
R using list.datasets for specific groups in h5 files
I have 4 groups within my h5 file such that the following code:
list.datasets(spot_sims)
= [1] "/Apple/2018" "/Apple/2019" "/IBM/2018" "/IBM/2019"
How can I query only the IBM group without having to use index numbers?
E.g. I have tried variations…
S_C
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