Extracts information on the VDJRegion level using MiXCR on WINDOWS, MAC and UNIX systems for input from both Platypus v2 (VDJ.per.clone) or v3 (Output of VDJ_GEX_matrix) This function assumes the user can run an executable instance of MiXCR and is elgible to use MiXCR as determined by license agreements. ! FOR WINDOWS USERS THE EXECUTABLE MIXCR.JAR HAS TO PRESENT IN THE CURRENT WORKING DIRECTORY ! In case the function is not able to call mixcr in "Windows" mode, please try setting the operating.system to "Linux". The VDJRegion corresponds to the recombined heavy and light chain loci starting from framework region 1 (FR1) and extending to frame work region 4 (FR4). This can be useful for extracting full-length sequences ready to clone and further calculating somatic hypermutation occurrences.
VDJ_call_MIXCR(
VDJ,
operating.system,
custom.cmd.call,
mixcr.directory,
species,
simplify,
platypus.version
)For platypus.version = "v2" the output from the VDJ_per_clone function. This object should have information regarding the contigs and clonotype_ids for each cell. For platypus.version = "v3" the VDJ dataframe output of the VDJ_GEX_matrix function (VDJ.GEX.matri.output[[1]])
Can be either "Windows", "Darwin" (for MAC) or "Linux". If left empty this is detected automatically
This function calls Mixcr via a terminal. The commands are build as follows: FOR DARWIN and LINUX machines: paste0(custom.cmd.call," ", mixcr.directory,"/mixcr.jar ... mixcr parameters assembled by function"). FOR WINDOWS machines: paste0(custom.cmd.call," mixcr.jar ... mixcr parameters assembled by function") custom.cmd.call defaults to "java -jar". In case different MIXCR installations, changing this to meet your systems requirements may be necessary.
The directory containing an executable version of MiXCR. FOR WINDOWS USERS THIS IS SET TO THE CURRENT WORKING DIRECTORY (please paste the content of the MIXCR folder after unzipping into your working directory. Make sure, that mixcr.jar is not within any subfolders.)
Either "mmu" for mouse or "hsa" for human. These use the default germline genes for both species contained in MIXCR. Defaults to "hsa"
Only relevant when platypus.version = "v3". Boolean. Defaults to TRUE. If FALSE the full MIXCR output and computed SHM column is appended to the VDJ If TRUE only the framework and CDR3 region columns and computed SHM column is appended. To discriminate between VDJ and VJ chains, prefixes are added to all MIXCR output columns
Character. Defaults to "v3". Can be "v2" or "v3" dependent on the input format
For platypus.version = "v3" returns input VDJ dataframe supplemented with MIXCR output information. For platypus.version = "v2" returns a nested list containing VDJRegion information as determined by MIXCR. The outer list corresponds to the individual repertoires in the same structure as the input VDJ.per.clone. The inner list corresponds to each clonal family, as determined by either the VDJ_clonotype function or the defaul nucleotide clonotyping produced by cellranger.Each element in the inner list corresponds to a dataframe containing repertoire information such as isotype, CDR sequences, mean number of UMIs. This output can be supplied to further package functions such as VDJ_extract_sequences and VDJ_GEX_integrate.
VDJ_extract_sequences
if (FALSE) {
#For platypus version 2
VDJ_call_MIXCR(VDJ = VDJ.per.clone.output,
mixcr.directory = "~/Downloads/mixcr-3.0.12/mixcr",species = "mmu")
#For platypus version 3 on a Windows system
VDJ_call_MIXCR(VDJ = VDJ_GEX_matrix.output[[1]],
mixcr.directory = "WILL BE SET TO CURRENT WORKING DIRECTORY",
species = "mmu", platypus.version = "v3", simplify = TRUE)
}