Error in `$<-.data.frame`(`*tmp*`, "feature", value = XXX) replacement has YYY rows, data has 0
0
0
Entering edit mode
3.4 years ago
cthangav ▴ 110

Hello, I have been trying to get this MOFA tutorial to work with my data set, but keep getting this error when the model is trained.

Error in `$<-.data.frame`(`*tmp*`, "feature", value = c("chr1:3514872-3515102",  : 


replacement has 131600 rows, data has 0

My code is very similar to the tutorial:

data <- fread("C:/Users/cathe/Desktop/NordenLab/Project/06172021 MEFISTO/Works/LongDataframe10Samples.txt")
data = data.frame(data)

#create MOFA Object
MOFAobject <- create_mofa(data)
MOFAobject
plot_data_overview(MOFAobject)

#Options
data_opts <- get_default_data_options(MOFAobject)
model_opts <- get_default_model_options(MOFAobject)
train_opts <- get_default_training_options(MOFAobject)

#Build Train MOFA Object
MOFAobject <- prepare_mofa(
  object = MOFAobject,
  data_options = data_opts,
  model_options = model_opts,
  training_options = train_opts
)

#Run MOFA
outfile = file.path(getwd(),"model.hdf5")
MOFAobject.trained <- run_mofa(MOFAobject, outfile)

So there is something wrong with my data.frame, which is formatted like this:

> data
    sample       feature        value view
1      MEF 0610005C13Rik 3.465742e-01  RNA
2      MEF 0610007P14Rik 4.508857e+01  RNA
3      MEF 0610009B22Rik 3.927700e+01  RNA
4      MEF 0610009L18Rik 3.487817e+00  RNA
5      MEF 0610009O20Rik 3.056666e+01  RNA
...
779921  iPSC5 chrY:90824242-90824507    31 ATAC
779922  iPSC5 chrY:90825138-90825545    38 ATAC
779923  iPSC5 chrY:90835583-90835832    19 ATAC
779924  iPSC5 chrY:90841589-90841857    31 ATAC
779925  iPSC5 chrY:90843869-90844126    16 ATAC

Any thoughts on how to resolve this error? Similar Error and Solution : https://stackoverflow.com/questions/64164612/error-in-data-framex-name-value-replacement-has-1-row-data-has-0

R • 4.8k views
ADD COMMENT
0
Entering edit mode

That is not just a data.frame, it's still a data.table - print(data.frame_obj) does not print the last few rows.. Maybe try using setDF(data).

ADD REPLY
0
Entering edit mode

thank you for the comment. I copy/pasted the last few rows by using the tail function. Sorry for the confusion, it didn't show up exactly like that when I printed it.

I ran the following code based on your recommendation to use setDF(), but still getting the same error.

data <- fread("C:/Users/cathe/Desktop/NordenLab/Project/06172021 MEFISTO/Works/LongDataframe10Samples.txt")
data = setDF(data)

#create MOFA Object
MOFAobject <- create_mofa(data)

#Data Options
data_opts <- get_default_data_options(MOFAobject)
model_opts <- get_default_model_options(MOFAobject)
train_opts <- get_default_training_options(MOFAobject)


#Build Train MOFA Object
MOFAobject <- prepare_mofa(
  object = MOFAobject,
  data_options = data_opts,
  model_options = model_opts,
  training_options = train_opts
)

outfile = file.path(getwd(),"model2.hdf5")
MOFAobject.trained <- run_mofa(MOFAobject, outfile)
ADD REPLY
1
Entering edit mode

In that case, the problem is not what I thought it was. Maybe someone else has a more productive lead. Sorry I couldn't help more.

EDIT: I meant to say "not what I thought it was", not "now what I thought it was" - changes the whole meaning, sorry about that!

ADD REPLY
0
Entering edit mode

Could you provide example data as dput(head(data))?

I am guessing you are getting the error after this step: MOFAobject <- create_mofa(data), I'd address the developers at GitHub (MOFA2/issues), most likely the input dataframe is not in the right format.

Error is easily reproducible as:

x <- data.frame()
x$a <- 1:3
# Error in `$<-.data.frame`(`*tmp*`, a, value = 1:3) : 
#   replacement has 3 rows, data has 0
ADD REPLY
0
Entering edit mode

So that error might be happening in the create_mofa() step?

Here is the dput(head(data))

> dput(head(data))
structure(list(sample = c("MEF", "MEF", "MEF", "MEF", "MEF", 
"MEF"), feature = c("0610005C13Rik", "0610007P14Rik", "0610009B22Rik", 
"0610009L18Rik", "0610009O20Rik", "0610010B08Rik"), value = c(0.346574178, 
45.08857437, 39.27700337, 3.487817488, 30.56665753, 0.021197777
), view = c("RNA", "RNA", "RNA", "RNA", "RNA", "RNA")), row.names = c(NA, 
6L), class = "data.frame")

Here is their example in the tutorial, which does not cause the same error:

    > dput(head(dt))
structure(list(sample = c("sample_0_group_0", "sample_1_group_0", 
"sample_2_group_0", "sample_3_group_0", "sample_4_group_0", "sample_5_group_0"
), group = c("group_0", "group_0", "group_0", "group_0", "group_0", 
"group_0"), feature = c("feature_0_view_0", "feature_0_view_0", 
"feature_0_view_0", "feature_0_view_0", "feature_0_view_0", "feature_0_view_0"
), view = c("view_0", "view_0", "view_0", "view_0", "view_0", 
"view_0"), value = c(-2.05, 0.1, 1.44, -0.28, -0.88, -1.18)), row.names = c(NA, 
-6L), class = c("data.table", "data.frame"), .internal.selfref = <pointer: 0x000001e4a5551ef0>)
ADD REPLY

Login before adding your answer.

Traffic: 1652 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