[R] you are making it far too difficult

[Sarah Goslee]

\t is the symbol for a tab.
/t is two characters just as it seems. It's highly unlikely your file
is delimited with /t, which would look like
1/t2/t3

The help for read.table mentions this tangentially as part of
read.delim(), and you can find out more under ?regex - see the section
about escaping non-metacharacters with a backslash.

Sarah

On Thu, Dec 27, 2018 at 4:09 PM Spencer Brackett
<spbrackett20 using saintjosephhs.com> wrote:
>
> What is the significance of using / or \ ?
>
> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee using gmail.com> wrote:
>>
>> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
>> <spbrackett20 using saintjosephhs.com> wrote:
>> >
>> > Thank you for the help! I tried using the read.table command in my RStudio
>> > using the following argument, and managed to open the file.
>> >
>> > GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)
>>
>> Note that sep="/t" is NOT the same thing as the sep="\t" you were
>> advised to use.
>>
>>
>>
>>
>> >
>> > However, my data did not unpack as yours did. I again only received a table
>> > of true and flase distinctions per column, and my environment tab says that
>> > there is 0 observations upon 0 variables.
>> >
>> > I believe I should be getting data similar to what you got, as it would
>> > appear that your’s actually contains relevant gene/protein expression info.
>> >
>> > On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
>> > federico.calboli using kuleuven.be> wrote:
>> >
>> > > Once you have your TSV files just use something as
>> > >
>> > > x = read.table('protein_expression.tsv', h = T, sep = '\t')
>> > >
>> > > Do not copy paste the code of this email because it is formatted and would
>> > > not work in R.
>> > >
>> > >
>> > > Best
>> > >
>> > > F
>> > >
>> > > PS the data looks like this to me
>> > >
>> > > head(x)
>> > >   icgc_donor_id project_code icgc_specimen_id icgc_sample_id
>> > >  submitted_sample_id analysis_id        antibody_id gene_name
>> > > 1       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765 14-3-3_epsilon-M-C     YWHAE
>> > > 2       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765         4E-BP1-R-V  EIF4EBP1
>> > > 3       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pS65-R-V  EIF4EBP1
>> > > 4       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT37-R-V  EIF4EBP1
>> > > 5       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765    4E-BP1_pT70-R-C  EIF4EBP1
>> > > 6       DO12370       GBM-US          SP26475       SA131594
>> > > TCGA-19-5960-01A-13-1900-20       97765          53BP1-R-C   TP53BP1
>> > >   gene_stable_id gene_build_version normalized_expression_level
>> > > verification_status verification_platform
>> > > 1             NA                 NA                  -1.1636330
>> > > not tested                    NA
>> > > 2             NA                 NA                  -1.7969721
>> > > not tested                    NA
>> > > 3             NA                 NA                  -0.7256390
>> > > not tested                    NA
>> > > 4             NA                 NA                   0.6498421
>> > > not tested                    NA
>> > > 5             NA                 NA                  -1.0262844
>> > > not tested                    NA
>> > > 6             NA                 NA                   1.5186400
>> > > not tested                    NA
>> > >                                         platform
>> > > 1 M.D. Anderson Reverse Phase Protein Array Core
>> > > 2 M.D. Anderson Reverse Phase Protein Array Core
>> > > 3 M.D. Anderson Reverse Phase Protein Array Core
>> > > 4 M.D. Anderson Reverse Phase Protein Array Core
>> > > 5 M.D. Anderson Reverse Phase Protein Array Core
>> > > 6 M.D. Anderson Reverse Phase Protein Array Core
>> > >
>> > >
>> > >
>> > > experimental_protocol
>> > > 1 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 2 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 3 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 4 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 5 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > > 6 MDA_RPPA_Core
>> > > http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>> > >   raw_data_repository          raw_data_accession
>> > > 1                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 2                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 3                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 4                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 5                TCGA TCGA-19-5960-01A-13-1900-20
>> > > 6                TCGA TCGA-19-5960-01A-13-1900-20
>> > >
>>
>>
>> --
>> Sarah Goslee (she/her)
>> http://www.numberwright.com