From 378363f1e2cf25de5865101cba1e66f03fc0662d Mon Sep 17 00:00:00 2001 From: leonjessen Date: Thu, 5 Sep 2024 09:30:02 +0200 Subject: [PATCH] Update lecture for lab 2 --- docs/lab02.html | 2 +- docs/lab05.html | 424 +++++++++--------- .../figure-html/unnamed-chunk-27-1.png | Bin 266236 -> 265579 bytes docs/primer_on_linear_models_in_r.html | 2 +- docs/search.json | 6 +- lab02.qmd | 2 +- pre_course_questionnaire_summary.html | 175 +++----- pre_course_questionnaire_summary.qmd | 120 ++--- 8 files changed, 317 insertions(+), 414 deletions(-) diff --git a/docs/lab02.html b/docs/lab02.html index 3d58ef6..4738de2 100644 --- a/docs/lab02.html +++ b/docs/lab02.html @@ -378,7 +378,7 @@

Package(s)

Schedule

@@ -1255,16 +1255,16 @@

C 
# A tibble: 10 × 11
    Experiment Cohort        Age Gender Race  A1    A2    B1    B2    C1    C2   
    <chr>      <chr>       <dbl> <chr>  <chr> <chr> <chr> <chr> <chr> <chr> <chr>
- 1 eHO130     Healthy (N…    28 F      White A*02… A*03… B*07… B*08… C*07… C*07…
- 2 eLH48      COVID-19-C…    28 M      White A*03… A*24… B*08… B*14… C*03… C*08…
- 3 eOX43      Healthy (N…    24 M      White A*02… A*03… B*27… B*40… C*03… C*07…
- 4 ePD76      Healthy (N…    33 M      White A*02… A*03… B*35… B*40… C*03… C*03…
- 5 eQD115     COVID-19-C…    48 M      <NA>  A*02… A*03… B*07… B*44… C*05… C*07…
- 6 eAV100     COVID-19-C…    29 F      <NA>  A*02… A*68… B*07… B*40… C*03… C*07…
- 7 eQD109     COVID-19-C…    61 M      <NA>  A*03… A*69… B*07… B*07… C*07… C*07…
- 8 eLH59      COVID-19-C…    NA <NA>   <NA>  A*01… A*02… B*40… B*52… C*03… C*16…
- 9 eMR15      COVID-19-C…    NA <NA>   <NA>  A*03… A*32… B*07… B*07… C*07… C*07…
-10 eAM23      COVID-19-C…    48 M      <NA>  A*11… A*24… B*15… B*52… C*04… C*12…
+ 1 eHO125 COVID-19-C… 52 M <NA> A*02… A*02… B*39… B*44… C*07… C*07… + 2 eHH169 Healthy (N… 24 F Blac… A*02… A*74… B*35… B*35… C*04… C*04… + 3 eHO129 COVID-19-C… 66 F Asian A*24… A*24… B*15… B*40… C*08… C*15… + 4 eLH47 COVID-19-C… 35 F White A*01… A*02… B*07… B*08… C*07… C*07… + 5 ePD85 Healthy (N… 27 F <NA> A*02… A*29… B*07… B*18… C*07… C*15… + 6 ePD80 COVID-19-C… 67 M <NA> A*02… A*66… B*15… B*41… C*03… C*17… + 7 eJL149 COVID-19-C… 60 F <NA> A*02… A*02… B*44… B*50… C*06… C*16… + 8 eQD109 COVID-19-C… 61 M <NA> A*03… A*69… B*07… B*07… C*07… C*07… + 9 eEE226 Healthy (N… 21 F White A*01… A*02… B*35… B*39… C*04… C*07… +10 eJL154 COVID-19-E… 35 F Nati… A*02… A*29… B*15… B*44… C*04… C*16…

Remember you can scroll in the data.

@@ -1285,16 +1285,16 @@

C 
# A tibble: 10 × 7
    Experiment Cohort                        Age Gender Race         Gene  Allele
    <chr>      <chr>                       <dbl> <chr>  <chr>        <chr> <chr> 
- 1 eLH47      COVID-19-Convalescent          35 F      White        A2    "A*02…
- 2 eJL160     COVID-19-Acute                 52 F      African Ame… B2    "B*81…
- 3 eAV100     COVID-19-Convalescent          29 F      <NA>         C2    "C*07…
- 4 eLH51      COVID-19-Convalescent          55 M      Asian        A1    "A*24…
- 5 eMR17      COVID-19-Convalescent          NA <NA>   <NA>         B2    "B*57…
- 6 eQD121     COVID-19-Convalescent          38 M      <NA>         C2    "C*07…
- 7 eNL192     COVID-19-Convalescent          NA <NA>   <NA>         C1    ""    
- 8 eMR23      COVID-19-Convalescent          22 F      <NA>         A1    ""    
- 9 eOX43      Healthy (No known exposure)    24 M      White        B1    "B*27…
-10 eLH42      COVID-19-Convalescent          63 M      <NA>         B1    "B*07…
+ 1 eDH107 COVID-19-Convalescent 72 F <NA> A2 "A*03… + 2 eQD117 COVID-19-Convalescent 70 F <NA> B1 "B*35… + 3 eAV100 COVID-19-Convalescent 29 F <NA> C1 "C*03… + 4 eHO138 COVID-19-B-Non-Acute NA <NA> <NA> A2 "" + 5 eJL149 COVID-19-Convalescent 60 F <NA> C1 "C*06… + 6 eMR25 COVID-19-Convalescent 21 F <NA> C1 "" + 7 eQD113 COVID-19-Convalescent 36 M <NA> A1 "A*03… + 8 eHH169 Healthy (No known exposure) 24 F Black or Af… A1 "A*02… + 9 eOX43 Healthy (No known exposure) 24 M White A1 "A*02… +10 eQD127 COVID-19-Convalescent 61 F <NA> C1 "C*02…

Remember, what we are aiming for here, is to create one data set from two. So:

@@ -1310,18 +1310,18 @@

C sample_n(10) 
# A tibble: 10 × 2
-   Experiment Allele      
-   <chr>      <chr>       
- 1 eJL157     "C*07:01:01"
- 2 eHO135     "B*07:02:01"
- 3 eHO141     ""          
- 4 eJL153     "A*03:01:01"
- 5 eMR20      "C*07:02:01"
- 6 eJL154     "B*15:02:01"
- 7 ePD82      "A*26:02:01"
- 8 eQD111     "A*01:01:01"
- 9 eMR22      "C*07:18:01"
-10 eJL146     "A*02:01"
+ Experiment Allele + <chr> <chr> + 1 eQD108 A*68:01:02 + 2 eHO130 B*08:01 + 3 ePD82 C*14:03:01 + 4 ePD83 C*03:04 + 5 eQD116 C*04:01:01 + 6 eQD123 A*02:01:01 + 7 eQD112 C*07:02:01 + 8 eOX43 C*03:04 + 9 eHO134 C*07:01:01 +10 eLH45 A*02:01:01

Use the View() function again, to look at the meta_data. Notice something? Some alleles are e.g. A*11:01, whereas others are B*51:01:02. You can find information on why, by visiting Nomenclature for Factors of the HLA System.

@@ -1347,16 +1347,16 @@

C 
# A tibble: 10 × 3
    Experiment Allele     Allele_F_1_2
    <chr>      <chr>      <chr>       
- 1 eJL157     C*07:02:01 C*07:02     
- 2 eQD118     C*03:04:01 C*03:04     
- 3 eMR13      C*07:01:01 C*07:01     
- 4 eLH54      B*40:02:01 B*40:02     
- 5 ePD82      C*08:01:01 C*08:01     
- 6 eQD121     B*57:01:01 B*57:01     
- 7 eAV88      C*07:04    C*07:04     
- 8 eDH105     B*40:01:02 B*40:01     
- 9 ePD86      C*14:02:01 C*14:02     
-10 eOX46      C*04:01    C*04:01
+ 1 eQD128 B*39:01:01 B*39:01 + 2 eOX46 A*02:01 A*02:01 + 3 eLH45 C*12:03:01 C*12:03 + 4 eQD120 A*31:01:02 A*31:01 + 5 ePD81 B*40:02:01 B*40:02 + 6 eXL27 C*07:04 C*07:04 + 7 ePD79 B*07:02:01 B*07:02 + 8 eDH105 A*24:02:01 A*24:02 + 9 eAV91 C*05:01 C*05:01 +10 eEE240 B*40:01 B*40:01

The asterisk, i.e. * is a rather annoying character because of ambiguity, so:

@@ -1373,16 +1373,16 @@

C 
# A tibble: 10 × 2
    Experiment Allele
    <chr>      <chr> 
- 1 eDH96      A02:01
- 2 eQD127     C02:02
- 3 eJL162     B55:01
- 4 eLH51      C12:04
- 5 eHO133     A32:01
- 6 eJL157     B18:01
- 7 eQD123     C07:02
- 8 eLH59      A02:01
- 9 eXL32      A01:01
-10 eLH45      C12:03
+ 1 eLH43 B44:03 + 2 eJL147 A11:01 + 3 eHH169 A02:01 + 4 eJL154 C16:01 + 5 eQD119 C07:01 + 6 eJL143 C08:02 + 7 eHH169 B35:01 + 8 eHO125 C07:01 + 9 eOX52 A02:01 +10 eLH48 B08:01
@@ -1407,18 +1407,18 @@

C sample_n(10) 
# A tibble: 10 × 7
-   Experiment CDR3b                  V_gene     J_gene peptide k_CDR3b k_peptide
-   <chr>      <chr>                  <chr>      <chr>  <chr>     <int>     <int>
- 1 eEE240     CASSQRSNTGELFF         TCRBV28-01 TCRBJ… AFLLFL…      14         9
- 2 eAV93      CATSDPPGWGQGAAYSNQPQHF TCRBV24-01 TCRBJ… TLACFV…      22        10
- 3 eOX54      CSASKLDSNNEQFF         TCRBV20-01 TCRBJ… SLIDFY…      14        10
- 4 eXL27      CASSPSGAGEQFF          TCRBV27-01 TCRBJ… FLWLLW…      13         9
- 5 eXL27      CASSDPFSGFYEQYF        TCRBV05-01 TCRBJ… VYFLQS…      15         9
- 6 eOX49      CASSGAGSNQPQHF         TCRBV09-01 TCRBJ… LLLDDF…      14         9
- 7 eEE228     CASRTGGSSYNEQFF        TCRBV19-01 TCRBJ… IELSLI…      15        10
- 8 eHO135     CASSLRSNQPQHF          TCRBV27-01 TCRBJ… ITLATC…      13         9
- 9 eEE226     CASSFSDYEQYF           TCRBV05-06 TCRBJ… FLNGSC…      12         9
-10 eHO124     CATSEALQETQYF          TCRBV24-01 TCRBJ… KVFRSS…      13         9
+ Experiment CDR3b V_gene J_gene peptide k_CDR3b k_peptide + <chr> <chr> <chr> <chr> <chr> <int> <int> + 1 eXL30 CASSLEISYEQYF TCRBV05-01 TCRBJ02-07 VPHVGEI… 13 11 + 2 eOX54 CASSASMSDTQYF TCRBV09-01 TCRBJ02-03 KLSYGIA… 13 9 + 3 eQD111 CASSELAGADTQYF TCRBV06-01 TCRBJ02-03 HTTDPSF… 14 11 + 4 eOX49 CSAHFPGQGFGEQFF TCRBV20-X TCRBJ02-01 YLCFLAF… 15 9 + 5 eHO128 CASSLQSPSSAGNEQFF TCRBV27-01 TCRBJ02-01 QSINFVR… 17 9 + 6 eOX49 CASSLWGDNEQFF TCRBV27-01 TCRBJ02-01 FYLCFLA… 13 9 + 7 eEE240 CASSFYSSGGAEGEQFF TCRBV27-01 TCRBJ02-01 LEYHDVR… 17 9 + 8 eEE228 CASSTKGRTNTGELFF TCRBV27-01 TCRBJ02-02 LIVNSVL… 16 10 + 9 eOX43 CASRGLAGDNSYEQYF TCRBV25-01 TCRBJ02-07 SLIDFYL… 16 10 +10 eOX52 CASSRGTGSEQYF TCRBV19-01 TCRBJ02-07 FLQSINF… 13 9