I want to gather methylation column from 100s of BS sequences files into a single file in a way that the first column should be the name of genes and the other 100 columns are the methylation value.
like:
Gene File1 File2 File3
NM_001 50 100 NA
NM_002 33.3 NA 100
for this i making a data frame and pasted the gene names in 1st column.It is done sucessfully.
When i try to paste methylation from 1st file by using logical indexing, it prints a new column but having NA
like:
Gene File1 File2 File3
NM_001 NA
NM_002 NA
I dont know how to do this.because when i use merging function it is taking too long to merge 2 files and also after 25 files it is not able to merge 2 files.
I have also changed the factor type into their appropriate data type but still not working
Can you paste an example of your code? For example I have in this example, a similar problem:
results=merge(experiment1,experiment2, by=1)
In this case I want to do a merge by the first column, which is one like Gene. Then, if I want to add another column I do:
results=merge(results, experiment3, by=1)
by the way, all the experiments table must have the same first column, which should correspond to the Genes.
Hi Ahsan,
As Luis said, it would be nice if you could write the code that you are using for us to tell you are doing right/wrong.
To answer to you question, the easy way would be to read the files as data frame and store them in a list. You can then merge them using a Reduce and merge function in R. something like the example below
merged.data=Reduce(function(...) merge(...,by="Gene", all=T), dataframe.list)
Hope it helps!
Thanks alot every one.Actually I have changed my function and now using aggregate that works well.
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