Question: problems in data frame
gravatar for niutster
3.2 years ago by
niutster100 wrote:

Dear all,

I have a two text files contain gene names and methylation degree. I have read these files with scan command in R and named them data1 and data2. Gene names and methylation degree have character and numeric type, respectively . when i combine them in one data frame with below command, it does not work correctly. All of them changes to a data frame with string type with number view and does not preserve their types.

df=data.frame(data1, data2)
R scan command data frame • 845 views
ADD COMMENTlink modified 3.1 years ago by Santosh Anand5.1k • written 3.2 years ago by niutster100

There's rarely a reason to use scan for such things, that's what read.delim() and such are for.

Please post a couple lines from data1 and data2 (or better yet, the original files before you read them in).

ADD REPLYlink written 3.2 years ago by Devon Ryan96k

1.) This is not a bioinformatics question.

2.) read the helps:

ADD REPLYlink written 3.2 years ago by h.mon31k
gravatar for Santosh Anand
3.1 years ago by
Santosh Anand5.1k
Santosh Anand5.1k wrote:

Try this

# install package data.table
data1 ="gene_names.txt"))
data2 ="methylation.txt"))
df = data.frame(data1, data2, stringsAsFactors = F)
ADD COMMENTlink written 3.1 years ago by Santosh Anand5.1k

You forgot to library(data.table). BTW, why do you need on data.table object (fread output)? Why not to:

data.table(gene = fread("gene.txt"), 
           meth = fread("meth.txt"))
ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by PoGibas4.8k

Yes, that's a much better way. In my mind, I was thinking to be as close to the OPs request as possible (so getting data1 and data2 as individual data.frames).

data.table can be quirky sometimes (e.g. column manipulation), although the class is both data.table and data.frame. Also, the printing of data.table is different.

ADD REPLYlink written 3.1 years ago by Santosh Anand5.1k
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