View all rows in R studio RNASeq

Question

[brandnewatthis]

This is definitely a basic question, but I can't seem to find a straight answer online. I am running DGE through R Studio and just calculated my normalization values, however, I have 12 lines of samples the the "e" command is only showing me 5 rows. What command can I use to few the last 7 rows of my $sample data?

[Jeremy]

What is the "e" command in R? In R Studio, in the Environment, you can click on the square to the right of your data to view all of it. Alternatively, you can simply type the name of your sample data in the console and hit ENTER.

Answer 1

[seidel]

There is no e command in base R. However, if your data is in an object with a $samples slot, chances are, that part of it is a dataframe. For instance, in edgeR if you have a DGEList object called y, the samples are stored in a dataframe called y$samples. To see all of them you can use indexes to specify the rows, or accessor functions like head() or tail().

y$samples[1:7,]
          group lib.size norm.factors
gd7_1         1 12749444    0.9974901
gd7_2         1 19512652    0.9246756
gd7_3         1 23624983    0.9972506
toll10b_1     2 17878014    1.0283200
toll10b_2     2 15778159    1.0571239
toll10b_3     2 17888014    1.0383200
toll10b_4     2 15438189    1.0172289

or use head() specify how many lines you'd like to see: head(y$samples, n=7)