diff --git a/docs/lab02.html b/docs/lab02.html index d2685d8..5cfe9e7 100644 --- a/docs/lab02.html +++ b/docs/lab02.html @@ -473,7 +473,7 @@

Getting Started

Then, before we start, we need to fetch some data to work on.

Then, without further ado, run each of the following lines separately in your console:

@@ -481,6 +481,14 @@

Getting Started

output_file <- "data/gravier.RData" curl::curl_download(url = target_url, destfile = output_file)
+
+

+

+Click here for a hint if you get an error along the lines of Failed to open file... + +

+Think about what we are doing here. If you look at the code chunk above, then you can see that we are setting a variable target_url, which defines “a location on the internet”. From here we want to download some data. We need to tell R, where to put this data, so we also define the output_file-variable. Then we call the function curl_download() from the curl-package, hence the notation curl::curl_download(). As arguments to the function-parameters url and destfile, we pass the aforementioned variables. So far so good. Now, look at the target_url- and the output_file-variables, which one of those are we responsible for? If you think about it - We cannot change the target_url, we can only change the output_file, so there is a good chance, that the error you are getting pertains to this variable. But what does the variable contain? It contains the path to where you want to place the file, that is the data/-part and then it contains the filename you want to use, that is the gravier-part and then finally, it contains the filetype you want to use, that is the .RData-part. The filename and filetype is up to you to choose, but the path… Well, R can only find that if it exists… So… Did you remember to create a folder data in the same location as your r_for_bio_data_science.Rproj-file? If this small intermezzo has left things even more unclear, you should go over the primer on paths and projects. Remember, if at first you don’t succeed - Try and try again! +
diff --git a/docs/lab05.html b/docs/lab05.html index f77a716..cec14cf 100644 --- a/docs/lab05.html +++ b/docs/lab05.html @@ -570,16 +570,16 @@

The Subject Meta Dat 
# A tibble: 10 × 30
    Experiment Subject `Cell Type` `Target Type` Cohort          Age Gender Race 
    <chr>        <dbl> <chr>       <chr>         <chr>         <dbl> <chr>  <chr>
- 1 eAV100        1995 PBMC        C19_cII       COVID-19-Con…    29 F      <NA> 
- 2 ePD86           92 PBMC        C19_cI        COVID-19-Con…    58 M      White
- 3 eTH332        2685 B-CD8-_PBMC C19_cII       COVID-19-Con…    NA <NA>   <NA> 
- 4 eMR13         2059 PBMC        C19_cI        COVID-19-Con…    NA <NA>   <NA> 
- 5 eQD119        5314 PBMC        C19_cI        COVID-19-Con…    51 M      <NA> 
- 6 ePD81         2922 PBMC        C19_cI        COVID-19-Con…    64 M      <NA> 
- 7 eHO131        3282 PBMC        C19_cI        COVID-19-Con…    58 F      <NA> 
- 8 eQD134        2903 PBMC        C19_cI        COVID-19-Con…    NA <NA>   <NA> 
- 9 eLH46          359 PBMC        C19_cI        COVID-19-Con…    57 F      White
-10 eHO124        3819 PBMC        C19_cI        Healthy (No …    62 M      <NA> 
+ 1 eJL148        3211 PBMC        C19_cI        COVID-19-Con…    41 F      <NA> 
+ 2 ePD91          169 PBMC        C19_cI        COVID-19-Con…    52 M      White
+ 3 eQD129        2283 PBMC        C19_cI        COVID-19-Con…    60 F      White
+ 4 eLH43         3565 PBMC        C19_cI        COVID-19-Con…    57 M      <NA> 
+ 5 eMR14         2845 PBMC        C19_cI        COVID-19-Con…    NA <NA>   <NA> 
+ 6 eQD135        6359 PBMC        C19_cII       COVID-19-Con…    74 M      <NA> 
+ 7 eQD115        2513 PBMC        C19_cI        COVID-19-Con…    48 M      <NA> 
+ 8 ePD84        19931 naive_CD8   C19_cI        Healthy (No …    29 F      Asian
+ 9 eJL152        7842 PBMC        C19_cI        COVID-19-Con…    41 F      <NA> 
+10 eJL162        6890 PBMC        C19_cI        COVID-19-Con…    61 M      <NA> 
 # ℹ 22 more variables: `HLA-A...9` <chr>, `HLA-A...10` <chr>,
 #   `HLA-B...11` <chr>, `HLA-B...12` <chr>, `HLA-C...13` <chr>,
 #   `HLA-C...14` <chr>, DPA1...15 <chr>, DPA1...16 <chr>, DPB1...17 <chr>,
@@ -643,16 +643,16 @@ 
The Peptide Detai
 
# A tibble: 10 × 7
    `TCR BioIdentity`            TCR Nucleotide Seque…¹ Experiment `ORF Coverage`
    <chr>                        <chr>                  <chr>      <chr>         
- 1 CASSLMGNQPQHF+TCRBV12-03/12… AAGATCCAGCCCTCAGAACCC… eOX56      envelope,ORF1…
- 2 CASSPGQGWDNEQFF+TCRBV07-07+… CAGCGCACAGAGCAGCGGGAC… eXL27      ORF3a         
- 3 CASSWDSSYEQYF+TCRBV07-02+TC… ACGATCCAGCGCACACAGCAG… ePD82      surface glyco…
- 4 VSVGEDQPQHF+TCRBV30-01+TCRB… ATCCTGAGTTCTAAGAAGCTC… eOX52      ORF1ab        
- 5 CASSRRNEKLFF+TCRBV06-06+TCR… CTCAGGCTGGAGTTGGCTGCT… eAV93      surface glyco…
- 6 CASSLGYEQFF+TCRBV07-08+TCRB… ACTCTGAAGATCCAGCGCACA… eLH47      surface glyco…
- 7 CASSQDWRVANTGELFF+TCRBV03-0… CTGGAGCTTGGTGACTCTGCT… eXL32      ORF7b         
- 8 CSVEAGTGFMQFF+TCRBV29-01+TC… ACTGTGAGCAACATGAGCCCT… eEE240     ORF10         
- 9 CASSPPVGGSYEQYF+TCRBV18-01+… CAGCAGGTAGTGCGAGGAGAT… eAM13      ORF3a         
-10 CASSPTDRVIGSAEQFF+TCRBV05-0… TTGGAGCTGGGGGACTCGGCC… eQD137     ORF1ab        
+ 1 CASSPQDRGASYEQYF+TCRBV18-01… CAGGTAGTGCGAGGAGATTCG… eOX52      ORF7b         
+ 2 unproductive+TCRBV11-02+TCR… TGCAAAGCTTGAGGACTCGGC… eHO141     nucleocapsid …
+ 3 CATVPDQNTGELFF+TCRBV10-02+T… CTGGAGTCAGCTACCCGCTCC… eHO141     surface glyco…
+ 4 CSARPGSRETQYF+TCRBV29-01+TC… ACTGTGAGCAACATGAGCCCT… eXL27      ORF3a         
+ 5 CASSPGQGAYEQYF+TCRBV04-02+T… CTACACACCCTGCAGCCAGAA… eXL27      ORF1ab        
+ 6 CASSLGFSVRTENTEAFF+TCRBV11-… AAGCTTGAGGACTCGGCCGTG… eOX56      ORF1ab        
+ 7 CSSPGPGYNEQFF+TCRBV29-01+TC… ACTGTGAGCAACATGAGCCCT… eOX43      ORF7a         
+ 8 CSAREEVKNYEQYF+TCRBV20-X+TC… GTGACCAGTGCCCATCCTGAA… eOX52      membrane glyc…
+ 9 CASSLTGETQYF+TCRBV07-03+TCR… CTGAAGATCCAGCGCACAGAG… eOX46      surface glyco…
+10 CASSLVLDVGIQYF+TCRBV07-09+T… ATCCAGCGCACAGAGCAGGGG… eAV93      ORF10         
 # ℹ abbreviated name: ¹​`TCR Nucleotide Sequence`
 # ℹ 3 more variables: `Amino Acids` <chr>, `Start Index in Genome` <dbl>,
 #   `End Index in Genome` <dbl>

@@ -937,18 +937,18 @@ 
The Peptide Detai
   sample_n(10)
# A tibble: 10 × 3
-   Experiment `TCR BioIdentity`                           `Amino Acids`         
-   <chr>      <chr>                                       <chr>                 
- 1 eXL31      CASSHYRGSYNEQFF+TCRBV03-01/03-02+TCRBJ02-01 FLQSINFVR,FLQSINFVRI,…
- 2 eOX43      CSASSLAEPKETQYF+TCRBV20-X+TCRBJ02-05        AFLLFLVLI,FLAFLLFLV,F…
- 3 eOX43      CASARLAGDTDTQYF+TCRBV16-01+TCRBJ02-03       FLNGSCGSV             
- 4 eOX52      CASSDLAGGLNEQFF+TCRBV09-01+TCRBJ02-01       AFPFTIYSL,GYINVFAFPF,…
- 5 eAV93      CASSTGQGWTEAFF+TCRBV05-06+TCRBJ01-01        CMTSCCSCLK,MTSCCSCLK  
- 6 eEE226     CASSPLQSNTEAFF+TCRBV05-01+TCRBJ01-01        AFLLFLVLI,FLAFLLFLV,F…
- 7 eOX54      CSVVLFGNEQFF+TCRBV29-01+TCRBJ02-01          FVDGVPFVV             
- 8 eEE240     CATYPLGGPPRDTEAFF+TCRBV15-01+TCRBJ01-01     FLNGSCGSV             
- 9 eOX56      CASSLGGATADEQFF+TCRBV07-03+TCRBJ02-01       KLPDDFTGCV            
-10 eXL31      CSARDLGRGSNEQFF+TCRBV20-X+TCRBJ02-01        AFLLFLVLI,FLAFLLFLV,F…
+ Experiment `TCR BioIdentity` `Amino Acids` + <chr> <chr> <chr> + 1 eEE226 CASSPWGAEDGYTF+TCRBV27-01+TCRBJ01-02 FLWLLWPVT,FLWLLWPVTL,LWLL… + 2 eEE224 CASSESGTPYNEQFF+TCRBV06-01+TCRBJ02-01 FVDGVPFVV + 3 eOX52 CASSQAGQPQHF+TCRBV07-06+TCRBJ01-05 FLCLFLLPSL,FLLPSLATV + 4 eOX52 CASSQDRAMLNEQFF+TCRBV04-03+TCRBJ02-01 SELVIGAVI,SELVIGAVIL + 5 eXL30 CASSQDSAGGSYNEQFF+TCRBV04-02+TCRBJ02-01 KLPDDFTGCV + 6 eAM23 CASSLVGRGTDTQYF+TCRBV05-05+TCRBJ02-03 DGVYFASTEK,GVYFASTEK,LPFN… + 7 eEE228 CASSPYPGLVVVDEQFF+TCRBV07-02+TCRBJ02-01 FVCNLLLLFV,LLFVTVYSHL,TVY… + 8 eXL30 CASSIGAGGTDTQYF+TCRBV19-01+TCRBJ02-03 AFLLFLVLI,FLAFLLFLV,FYLCF… + 9 eEE228 CASRGFTVYNEQFF+TCRBV11-02+TCRBJ02-01 AFLLFLVLI,FLAFLLFLV,FYLCF… +10 ePD83 CASSSGQGVSYEQYF+TCRBV19-01+TCRBJ02-07 SEHDYQIGGYTEKW,YQIGGYTEK,…