Platypus (version 3.6.0)

PlatypusDB_load_from_disk: PlatypusDB utility for import of local datasets

Description

Utility function for loading in local dataset as VDJ_GEX_matrix and PlatypusDB compatible R objects. Especially useful when wanting to integrate local and public datasets. This function only imports and does not make changes to format, row and column names. Exception: filtered_contig.fasta are appended to the filtered_contig_annotations.csv as a column for easy access

Usage

PlatypusDB_load_from_disk(
  VDJ.out.directory.list,
  GEX.out.directory.list,
  FB.out.directory.list,
  batches
)

Value

Large nested list object containing all needed Cellranger outputs to run the VDJ_GEX_matrix function. Level 1 of the list are samples, level 2 are VDJ GEX and metadata information. (e.g. out[[1]][[1]] corresponds to VDJ data objects of sample 1)

Arguments

VDJ.out.directory.list

List containing paths to VDJ output directories from cell ranger. This pipeline assumes that the output file names have not been changed from the default 10x settings in the /outs/ folder. This is compatible with B and T cell repertoires (both separately and simultaneously).

GEX.out.directory.list

List containing paths the outs/ directory of each sample or directly the raw or filtered_feature_bc_matrix folder. Order of list items must be the same as for VDJ. This outs directory may also contain Feature Barcode (FB) information. Do not specify FB.out.directory in this case.

FB.out.directory.list

List of paths pointing at the outs/ directory of output of the Cellranger counts function which contain Feature barcode counts. Any input will overwrite potential FB data loaded from the GEX input directories. Length must match VDJ and GEX directory inputs. (in case of a single FB output directory for multiple samples, please specifiy this directory as many times as needed)

batches

Integer vector. Defaults to all 1, yielding all samples with batch number "b1". Give a batch number to each sample (each entry in the VDJ/GEX input lists). This will be saved as element 5 in the sample list output.

Examples

# \donttest{
try({
VDJ.in <- list()
VDJ.in[[1]] <- c("~/VDJ/S1/")
VDJ.in[[2]] <- c("~/VDJ/S2/")
GEX.in <- list()
GEX.in[[1]] <- c("~/GEX/S1/")
GEX.in[[2]] <- c("~/GEX/S2/")
PlatypusDB_load_from_disk(VDJ.out.directory.list = VDJ.in, GEX.out.directory.list = GEX.in)
})
# }