From b92d6e19c40f2c17808cd224beaa1a2ef9586ae5 Mon Sep 17 00:00:00 2001 From: leonjessen Date: Tue, 22 Oct 2024 14:33:21 +0200 Subject: [PATCH] Update lab 10 description --- docs/lab05.html | 416 +++++++++--------- .../figure-html/unnamed-chunk-27-1.png | Bin 267948 -> 265995 bytes docs/lab10.html | 3 +- docs/primer_on_linear_models_in_r.html | 2 +- docs/search.json | 6 +- lab10.qmd | 4 +- 6 files changed, 217 insertions(+), 214 deletions(-) diff --git a/docs/lab05.html b/docs/lab05.html index 53651eb..237ee67 100644 --- a/docs/lab05.html +++ b/docs/lab05.html @@ -566,16 +566,16 @@

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 ePD85         5869 naive_CD8   C19_cI        Healthy (No …    27 F      <NA> 
- 2 ePD81         2922 PBMC        C19_cI        COVID-19-Con…    64 M      <NA> 
- 3 eQD129        2283 PBMC        C19_cI        COVID-19-Con…    60 F      White
- 4 eHO125        4611 PBMC        C19_cI        COVID-19-Con…    52 M      <NA> 
- 5 eNL192        1524 B-CD8-_PBMC C19_cII       COVID-19-Con…    NA <NA>   <NA> 
- 6 eJL151        3270 PBMC        C19_cI        COVID-19-Con…    79 F      <NA> 
- 7 eHO126        6913 PBMC        C19_cI        COVID-19-Con…    37 F      <NA> 
- 8 eQD124         361 PBMC        C19_cI        COVID-19-B-N…    40 F      White
- 9 eQD136        2818 PBMC        C19_cI        COVID-19-Con…    NA <NA>   <NA> 
-10 eXL31        20300 naive_CD8   C19_cI        Healthy (No …    28 M      White
+ 1 eLH43         3565 PBMC        C19_cI        COVID-19-Con…    57 M      <NA> 
+ 2 eQD134        2903 PBMC        C19_cI        COVID-19-Con…    NA <NA>   <NA> 
+ 3 ePD100        1811 PBMC        C19_cI        COVID-19-Con…    66 M      <NA> 
+ 4 eAV100        1995 PBMC        C19_cII       COVID-19-Con…    29 F      <NA> 
+ 5 ePD91          169 PBMC        C19_cI        COVID-19-Con…    52 M      White
+ 6 eHO133     1005699 PBMC        C19_cI        COVID-19-Acu…    67 M      White
+ 7 eHO129         142 PBMC        C19_cI        COVID-19-Con…    66 F      Asian
+ 8 eMR22      1565927 PBMC        C19_cI        COVID-19-Con…    65 M      <NA> 
+ 9 eMR14         2845 PBMC        C19_cI        COVID-19-Con…    NA <NA>   <NA> 
+10 eQD124         361 PBMC        C19_cI        COVID-19-B-N…    40 F      White
 # 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>,
@@ -639,16 +639,16 @@
+ 1 eEE217 Healthy (N… 32 F White "A*0… "A*0… "B*1… "B*4… "C*0… "C*0… + 2 eLH41 COVID-19-C… 71 F <NA> "A*0… "A*0… "B*1… "B*1… "C*0… "C*0… + 3 ePD73 Healthy (N… 37 F White "A*0… "A*0… "B*1… "B*4… "C*0… "C*0… + 4 eHO136 COVID-19-C… 51 M Hisp… "" "" "" "" "" "" + 5 eHO125 COVID-19-C… 52 M <NA> "A*0… "A*0… "B*3… "B*4… "C*0… "C*0… + 6 eOX46 Healthy (N… 45 M White "A*0… "A*0… "B*3… "B*4… "C*0… "C*0… + 7 eQD113 COVID-19-C… 36 M <NA> "A*0… "A*1… "B*5… "B*5… "C*0… "C*1… + 8 eOX56 Healthy (N… 30 M Blac… "A*0… "A*3… "B*5… "B*5… "C*0… "C*0… + 9 eQD108 COVID-19-C… NA <NA> <NA> "A*1… "A*6… "B*0… "B*5… "C*0… "C*1… +10 eXL43 Healthy (N… 36 F White "A*3… "A*3… "B*0… "B*1… "C*0… "C*0…

Now, we have a beautiful tidy dataset, recall that this entails, that each row is an observation, each column is a variable and each cell holds one value.

@@ -888,16 +888,16 @@

The Peptide Detai 
# A tibble: 10 × 7
    `TCR BioIdentity`            TCR Nucleotide Seque…¹ Experiment `ORF Coverage`
    <chr>                        <chr>                  <chr>      <chr>         
- 1 unproductive+TCRBV03-01/03-… TCACATCAATTCCCTGGAGCT… eHO141     surface glyco…
- 2 CASSRRDMGGGPTDTQYF+TCRBV19-… CAAAAGAACCCGACAGCTTTC… eEE226     ORF7b         
- 3 CSASLESETQYF+TCRBV20-01+TCR… CTGACAGTGACCAGTGCCCAT… eEE226     ORF7b         
- 4 CASSLTGALGRSIANQPQHF+TCRBV1… AGGGACTCAGCTGTGTACTTC… eXL31      ORF3a         
- 5 CASRKGSTNEKLFF+TCRBV05-06+T… GTGAACGCCTTGTTGCTGGGG… eEE226     ORF7b         
- 6 CASSPGLVIEQFF+TCRBV13-01+TC… AACATGAGCTCCTTGGAGCTG… eHO136     ORF1ab        
- 7 CASTPGLAVYEQYF+TCRBV12-X+TC… ATCCAGCCCTCAGAACCCAGG… eEE228     ORF1ab        
- 8 CSARAGGYSNQPQHF+TCRBV20-X+T… ACCAGTGCCCATCCTGAAGAC… eOX52      surface glyco…
- 9 CASSPDWGGGEQYF+TCRBV05-04+T… GTGAACGCCTTGGAGCTGGAC… eEE228     ORF1ab        
-10 CASDEGVDNEQFF+TCRBV02-01+TC… AAGATCCGGTCCACAAAGCTG… eEE226     surface glyco…
+ 1 CASSLWASGPNEQFF+TCRBV28-01+… GAGTCCGCCAGCACCAACCAG… eHH175     surface glyco…
+ 2 CASSPQGSLTEAFF+TCRBV06-05+T… NNNNTGTCGGCTGCTCCCTCC… eQD126     ORF1ab        
+ 3 CASSVGQGVIAGGPSEQFF+TCRBV09… CTGGGGGACTCAGCTTTGTAT… eOX52      ORF1ab        
+ 4 CASSPQLAMRGNEQFF+TCRBV07-08… CGCACACAGCAGGAGGACTCC… eQD124     membrane glyc…
+ 5 CASSFTTGAGANVLTF+TCRBV05-04… GCCTTGGAGCTGGACGACTCG… eEE226     surface glyco…
+ 6 CSATGRAGINEQFF+TCRBV20-X+TC… GTGACCAGTGCCCATCCTGAA… eEE240     ORF1ab        
+ 7 CSASLGLYEQYF+TCRBV20-01+TCR… CTGACAGTGACCAGTGCCCAT… eOX49      ORF1ab        
+ 8 CASSFGQVGQPQHF+TCRBV28-01+T… CTGGAGTCCGCCAGCACCAAC… eXL31      membrane glyc…
+ 9 CSVGTGDGETQYF+TCRBV20-X+TCR… ACAGTGACCAGTGCCCATCCT… eXL32      ORF7b         
+10 CSADTRGVEETQYF+TCRBV20-X+TC… GTGACCAGTGCCCATCCTGAA… eLH49      ORF1ab        
 # ℹ abbreviated name: ¹​`TCR Nucleotide Sequence`
 # ℹ 3 more variables: `Amino Acids` <chr>, `Start Index in Genome` <dbl>,
 #   `End Index in Genome` <dbl>
@@ -933,18 +933,18 @@

The Peptide Detai sample_n(10) 
# A tibble: 10 × 3
-   Experiment `TCR BioIdentity`                       `Amino Acids`             
-   <chr>      <chr>                                   <chr>                     
- 1 eLH51      CASSTSGNTGELFF+TCRBV19-01+TCRBJ02-02    APSASAFFGM,AQFAPSASA,ASAF…
- 2 eHO140     CASNDLNTGELFF+TCRBV02-01+TCRBJ02-02     YLQPRTFL,YLQPRTFLL,YYVGYL…
- 3 eEE240     CSASGSLIGTNEKLFF+TCRBV20-X+TCRBJ01-04   AFLLFLVLI,FLAFLLFLV,FYLCF…
- 4 eEE240     CSLALADPDTQYF+TCRBV29-01+TCRBJ02-03     DFLEYHDVR,EDFLEYHDVR,LEYH…
- 5 eMR23      CSARGWGGPKTSTDTQYF+TCRBV20-X+TCRBJ02-03 ALNTPKDHI,ATEGALNTPK      
- 6 eOX54      CASSQGVGTEAFF+TCRBV04-03+TCRBJ01-01     AFPFTIYSL,GYINVFAFPF,INVF…
- 7 eOX49      CASSLGQGAYEQYF+TCRBV04-01+TCRBJ02-07    FLNGSCGSV                 
- 8 eEE224     CASSQDLGMGEQFF+TCRBV06-X+TCRBJ02-01     TVLSFCAFA,VLSFCAFAV       
- 9 eHH175     CASSQPSYEQYF+TCRBV04-02+TCRBJ02-07      AFLLFLVLI,FLAFLLFLV,FYLCF…
-10 eMR15      CASDQTGGRGTDTQYF+TCRBV28-01+TCRBJ02-03  FPRGQGVPI,KFPRGQGVPI
+ Experiment `TCR BioIdentity` `Amino Acids` + <chr> <chr> <chr> + 1 eQD137 CASSPLDEDEAFF+TCRBV18-01+TCRBJ01-01 HTTDPSFLGRY + 2 eQD112 CASS*PED*RGLNRDTQYF+TCRBV13-01+TCRBJ02-03 LSPRWYFYY,SPRWYFYYL + 3 eQD131 CASSLSGAPGVGTDTQYF+TCRBV05-06+TCRBJ02-03 FLQSINFVR,FLQSINFVRI,… + 4 eDH105 CASSRTGTGPYEQYF+TCRBV28-01+TCRBJ02-07 ALALLLLDR,GDAALALLLL,… + 5 eEE224 RASSLESYNEQFF+TCRBV07-03+TCRBJ02-01 AFPFTIYSL,GYINVFAFPF,… + 6 eOX54 CASSLGGVTGGELFF+TCRBV04-02+TCRBJ02-02 YLDAYNMMI + 7 eEE228 CASSPVTGTNQPQHF+TCRBV03-01/03-02+TCRBJ01-05 AFLLFLVLI,FLAFLLFLV,F… + 8 eQD121 CASSLSSSQETQYF+TCRBV27-01+TCRBJ02-05 HTTDPSFLGRY + 9 eXL30 CASSYSAAANTGELFF+TCRBV06-06+TCRBJ02-02 AEAELAKNVSL,AELAKNVSL… +10 eLH47 CASSPDIQAFF+TCRBV07-09+TCRBJ01-01 YLQPRTFL,YLQPRTFLL,YY…