From 97b8914cd52f544a77e9925a01509466b9af30ee Mon Sep 17 00:00:00 2001 From: coolneng Date: Tue, 23 Mar 2021 18:24:01 +0100 Subject: [PATCH] Add literate programming notebook --- docs/notebook.org | 46 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 docs/notebook.org diff --git a/docs/notebook.org b/docs/notebook.org new file mode 100644 index 0000000..5b8a08e --- /dev/null +++ b/docs/notebook.org @@ -0,0 +1,46 @@ +#+TITLE: locigenesis +#+AUTHOR: Amin Kasrou Aouam +#+DATE: 2021-03-10 +* Sequence alignment + +Our generated sequences contain the full VJ region, but we are only interested in the CDR3 (Complementarity-determining region). We will proceed by delimiting CDR3, using the known sequences of V and J. + +#+begin_src R :results value silent +v_segments <- readRDS("data/v_segments.rds") +j_segments <- readRDS("data/j_segments_phe.rds") +#+end_src + +#+begin_src R +print(v_segments) +print(j_segments) +#+end_src + +#+RESULTS: +#+begin_example + A DNAStringSet instance of length 147 + width seq names + [1] 326 GATACTGGAATTACCCAGACAC...ATCTCTGCACCAGCAGCCAAGA TRBV1*01_P + [2] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*01_F + [3] 326 GATGCTGAAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-1*02_F + [4] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*01_F + [5] 326 GATGCTGGAATCACCCAGAGCC...ATTTCTGCGCCAGCAGTGAGTC TRBV10-2*02_F + ... ... ... +[143] 324 GATACTGGAGTCTCCCAGAACC...GTATCTCTGTGCCAGCACGTTG TRBV7-9*06_(F) +[144] 323 .........................TGTATCTCTGTGCCAGCAGCAG TRBV7-9*07_(F) +[145] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*01_F +[146] 325 GATTCTGGAGTCACACAAACCC...TATTTCTGTGCCAGCAGCGTAG TRBV9*02_F +[147] 321 GATTCTGGAGTCACACAAACCC...TTTGTATTTCTGTGCCAGCAGC TRBV9*03_(F) + A DNAStringSet instance of length 16 + width seq names + [1] 32 TGGGCGTCTGGGCGGAGGACTCCTGGTTCTGG TRBJ2-2P*01_ORF + [2] 31 TTTGGAGAGGGAAGTTGGCTCACTGTTGTAG TRBJ1-3*01_F + [3] 31 TTTGGTGATGGGACTCGACTCTCCATCCTAG TRBJ1-5*01_F + [4] 31 TTTGGCAGTGGAACCCAGCTCTCTGTCTTGG TRBJ1-4*01_F + [5] 31 TTCGGTTCGGGGACCAGGTTAACCGTTGTAG TRBJ1-2*01_F + ... ... ... +[12] 31 TTTGGCCCAGGCACCCGGCTGACAGTGCTCG TRBJ2-3*01_F +[13] 31 TTCGGGCCAGGCACGCGGCTCCTGGTGCTCG TRBJ2-5*01_F +[14] 31 TTCGGGCCAGGGACACGGCTCACCGTGCTAG TRBJ2-1*01_F +[15] 31 TTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*01_F +[16] 31 GTCGGGCCGGGCACCAGGCTCACGGTCACAG TRBJ2-7*02_ORF +#+end_example