run_TRIP: Run tripr analysis via R command line

In iofeidis/tripr: T-cell Receptor/Immunoglobulin Profiler (TRIP)

Description

run_TRIP() is a wrapper of {tripr} shiny analysis tool for use via R command line. Output of analysis is saved in tripr/extdata/output folder, where R libraries are saved (typically R/library).

Usage

run_TRIP(
  datapath = fs::path_package("extdata", "dataset", package = "tripr"),
  output_path = fs::path_home("Documents/tripr_output"),
  filelist = c("1_Summary.txt", "2_IMGT-gapped-nt-sequences.txt",
    "4_IMGT-gapped-AA-sequences.txt", "6_Junction.txt"),
  cell = "Bcell",
  throughput = "High Throughput",
  preselection = "1,4C:W",
  selection = "5",
  identity_range = "85:100",
  vgenes = "",
  dgenes = "",
  jgenes = "",
  cdr3_length_range = "",
  aminoacid = "",
  pipeline = "1",
  select_clonotype = "V Gene + CDR3 Amino Acids",
  highly_sim_params = paste0("1-1 2-1 3-1 4-1 5-1 6-1 7-1 8-1 9-1 10-1 11-1 ",
    "12-1 13-1 14-1 15-2 16-2 17-2 18-2 19-2 20-2 21-2 23-2 24-2 25-2 ",
    "26-2 27-2 28-2 29-3 30-3 31-3 32-3 33-3 34-3 35-3 36-3 37-3 38-3 ",
    "39-3 40-3 41-3 42-3 43-3 44-3 45-3 46-3 47-3 48-3 49-3 50-3,1,Yes"),
  shared_clonotypes_params = "reads,1,Yes",
  highly_shared_clonotypes_params = "reads,1,Yes",
  repertoires_params = "1,4,6",
  identity_groups = "85:97,97:99,99:100,100:100",
  multiple_values_params = "2:7,2:3,2:5,2:11",
  alignment_params = "1,both,1,2:20",
  mutations_params = "both,0.5,0.5,2:20"
)

Arguments

datapath	(character) The directory where the folders of the data is located. Note that every sample of the dataset must have its own individual folder and every sample folder must be in one root folder. Note that every file in the root folder will be used in the analysis. Supposedly the dataset is in user's Documents/ folder, one could use: fs::path_home("Documents", "dataset"), with the help of path_home function. See the package vignette for more.
output_path	(character) The directory where the output data will be stored. Please provide a valid path, ideally the same way as datapath by using the path_home function. The default value points to Documents/tripr_output directory.
filelist	(character vector) The character vector of files of the IMGT output that will be used through the analysis from each sample.
cell	(character) 'Bcell' (default) or 'Tcell'.
throughput	(character) 'High Throughput' (default) or 'Low Throughput'.
preselection	(character) Preselection options: 1 == Only take into account Functional V-Gene, 2 == Only take into account CDR3 with no Special Characters (X,*,#,.), 3 == Only take into account Productive Sequences, 4 == Only take into account CDR3 with valid start/end landmarks., For Preselection option 4, select start/end landmarks., Use the vertical line '|' to add more than one start or end landmarks, Use comma ',' to seperate the list of options, use semicolon ':' to seperate start and end landmarks.
selection	(character) Selection options: 5 == V-REGION identity 6 == Select Specific V Gene , 7 == Select Specific J Gene , 8 == Select Specific D Gene , 9 == Select CDR3 length range , 10 == Only select CDR3 containing specific amino-acid sequence. Use comma ',' to seperate the list of options.
identity_range	(character) V-REGION identity Use colon ':' to seperate identity low and high
vgenes	(character) Filter in specific V Genes, Separate the different V-Gene names with '|' e.g. TRBV11-2|TRBV29-1*03 (F)
dgenes	(character) Filter in specific D Genes, Separate the different D-Gene names with | e.g. TRBD2|TRBD1
jgenes	(character) Filter in specific J Genes, Separate the different J-Gene names with | e.g. TRBJ2-6|TRBJ2-2
cdr3_length_range	(character) Filter in rows with CDR3 lengths within a range, Use colon ':' to seperate identity low and high
aminoacid	(character) Filter in rows with CDR3 containing specific amino-acid sequence
pipeline	(character) Pipeline options: 1 == Clonotypes Computation, 2 == Highly Similar Clonotypes computation, 3 == Shared Clonotypes Computation, 4 == Highly Similar Shared Clonotypes Computation, 5 == Repertoires Extraction, 6 == Repertoires Comparison, 7 == Highly Similar Repertoires Extraction, 8 == Insert Identity groups, 9 == Somatic hypermutation status, 10 == CDR3 Distribution, 11 == Pi Distribution, 12 == Multiple value comparison, 13 == CDR3 with 1 length difference, 14 == Alignment, 15 == Somatic hypermutations, 16 == Logo, 17 == SHM normal, 18 == SHM High similarity, 19 == Diagnosis, Use comma ',' to seperate the list of options
select_clonotype	(character) Compute clonotypes. Select one the following options: "V Gene + CDR3 Amino Acids", "V Gene and Allele + CDR3 Amino Acids", "V Gene + CDR3 Nucleotide", "V Gene and Allele + CDR3 Nucleotide", "J Gene + CDR3 Amino Acids", "J Gene and Allele + CDR3 Amino Acids", "J Gene + CDR3 Nucleotide", "J Gene and Allele + CDR3 Nucleotide", "CDR3 Amino Acids", "CDR3 Nucleotide", "Sequence
highly_sim_params	(character) Select number of missmatches, the threshold of the clonotype frequency and whether you want to take gene into account. Use dashes '-' to show the length of the CDR3 sequences and the number of allowed missmatches and spaces ' ' to separate. For the CDR3 lengths with not specified number of missmatches the default value is 1. Use comma ',' to separate the three options.
shared_clonotypes_params	(character) Shared clonotypes computation. Select 'reads' of 'threshold' for clonotypes, the number of reads or the threshold percentage accordingly, and whether you want to take gene into account. Use comma ',' to seperate the 3 options
highly_shared_clonotypes_params	(character) Highly Similar Shared Clonotypes Computation Select 'reads' of 'threshold' for clonotypes, the number of reads or the threshold percentage accordingly, and whether you want to take gene into account. Use comma ',' to seperate the 3 options
repertoires_params	(character) Repertoires Extraction Options: 1 == V Gene 2 == V Gene and allele 3 == J Gene 4 == J Gene and allele 5 == D Gene 6 == D Gene and allele Use comma ',' to seperate the selected options
identity_groups	(character) Insert identity groups Insert low and high values as follows: low_values:high_values Seperate low_values and high_values using comma ','.
multiple_values_params	(character) Multiple value comparison Options: 1 == V GENE 2 == V GENE and allele 3 == J GENE 4 == J GENE and allele 5 == D GENE 6 == D GENE and allele 7 == CDR3-IMGT length 8 == D-REGION reading frame 9 == Molecular mass 10 == pI 11 == V-REGION identity Use colon ':' to indicate combinations of 2 values, use comma "," to seperate the selected options
alignment_params	(character) Alignment parameters: Region for Alignment: 1 == V.D.J.REGION or 2 == V.J.REGION AA or Nt: Select 'aa' or 'nt' or 'both' Germline: 1 == Use Allele's germline or 2 == Use Gene's germline Use: 1 == All clonotypes or 2 == Select top N clonotypes or 3 == Select threshold for clonotypes Use comma ',' to seperate the 4 parameters. If you select option 2 or 3 at the 4th parameter you have to set the N or the threshold as well using colon ':'.
mutations_params	(character) Somatic hypermutations parameters: AA or Nt: Select 'aa' or 'nt' or 'both' Set threshold for AA Set threshold for Nt Use: 1 == All clonotypes or 2 == Select top N clonotypes or 3 == Select threshold for clonotypes Use comma ',' to seperate the 3 parameters. If you select option 2 or 3 at the 3rd parameter you have to set the N or the threshold as well using colon ':'.

Value

None

Examples

## Do not run

run_TRIP(
   output_path=fs::path_home("Documents/my_output"),
   filelist=c("1_Summary.txt", "2_IMGT-gapped-nt-sequences.txt", 
       "4_IMGT-gapped-AA-sequences.txt", "6_Junction.txt"),
   cell="Bcell", 
   throughput="High Throughput", 
   preselection="1,2,3,4C:W", 
   selection="5", 
   identity_range="88:100", 
   cdr3_length_range="", 
   pipeline="1", 
   select_clonotype="V Gene + CDR3 Amino Acids")

iofeidis/tripr documentation built on Dec. 20, 2021, 7:58 p.m.