How to move Trinity data into RStudio

Question

[hydra_questions]

I'm using trinity to do a de novo transcriptome assembly + DGE analysis. The problem is I need to conduct a more complicated analysis than the simple pairwise DE set up provided in the Trinity software.

The count matrix has a .matrix suffix so RStudio is not letting me import. I was wondering if anyone knew how to upload the matrices produced by Trinity into RStudio.

Thanks in advance!

[Ram]

What is the output of:

file <your_file_name>.matrix
head <your_file_name>.matrix

[hydra_questions]

file Trinity_genes.counts.matrix
Trinity_genes.counts.matrix: ASCII text, with very long lines

head Trinity_genes.counts.matrix
        CB1_L1  CB1_L2  CB2_L1  CB2_L2  CB3_L1  CB3_L2  CD1_L1  CD1_L2  CD2_L1  CD2_L2  CD3_L1  CD3_L2  RA1_L1  RA1_L2 RA2_L1                                          RA2_L2   RA3_L1  RA3_L2  SIRT1_L1        SIRT1_L2        SIRT2_L1        SIRT2_L2        SIRT3_L1        SIRT3_L2       SALB1_L1                                        SALB1_L2 SALB2_L1        SALB2_L2        SALB3_L1        SALB3_L2        SALD1_L1        SALD1_L2        SALD2_L1       SALD2_L2                                        SALD3_L1 SALD3_L2        PCIB1_L1        PCIB1_L2        PCIB2_L1        PCIB2_L2        PCIB3_L1        PCIB3_L2       PCID1_L1                                        PCID1_L2 PCID2_L1        PCID2_L2        PCID3_L1        PCID3_L2
TRINITY_DN50647_c0_g1   0.00    0.00    1.00    1.00    0.00    0.00    0.00    0.00    1.00    0.00    0.00    0.00   0.00                                            1.00     0.00    0.00    0.00    0.00    0.00    0.00    0.00    1.00    0.00    0.00    0.00    0.00    0.00    0.00   0.00                                            0.00     0.00    0.00    0.00    0.00    0.00    0.00    1.00    1.00    0.00    0.00    0.00    0.00    0.00    0.00   0.00                                            1.00     0.00    0.00
TRINITY_DN90316_c0_g1   1.00    0.00    0.00    0.00    0.00    0.00    1.00    0.00    0.00    0.00    0.00    1.00   0.00                                            1.00     0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    1.00    1.00   0.00                                            0.00     0.00    0.00    3.00    1.00    0.00    0.00    0.00    1.00    1.00    1.00    0.00    0.00    0.00    0.00   0.00                                            0.00     1.00    0.00
TRINITY_DN99724_c0_g1   23.00   12.00   23.00   21.00   17.00   10.00   15.00   22.00   20.00   14.00   24.00   26.00  20.00                                           15.00    29.00   33.00   21.00   20.00   17.00   17.00   28.00   24.00   19.00   22.00   27.00   21.00   16.00   16.00  15.00                                           25.00    25.00   21.00   25.00   10.00   27.00   23.00   21.00   5.00    28.00   24.00   25.00   19.00   22.00   16.00  18.00                                           26.00    36.00   31.00

[Ram]

If the columns are tab-separated, you should be able to use read.table(file, sep="\t", header = TRUE)