read_cellranger_outs: Read necessary file from 10X Genomics' cellranger output and...
In Close-your-eyes/igsc: Immunoglobolin sequences from scRNAseq
View source: R/read_cellranger_outs.R
read_cellranger_outs R Documentation
Read necessary file from 10X Genomics' cellranger output and return a concatenated data frame
Description
Caution: This function will add CDR3 sequences etc. uniformly to equal clonotype_ids even though
if e.g. TRA was detected in every cell that has been assigned with clonotype_id i.
Use read_cellranger_outs2 for a different behaviour, namely that this kind of
imputation is not performed.
Usage
read_cellranger_outs(vdj_path)
Arguments
vdj_path
path to the parent folder containing one or multiple subfolders with cellrangers VDJ outs
Details
Required files in each subfolder of vdj_path are consensus_annotations.csv, filtered_contig_annotations.csv, consensus.fasta, concat_ref.fasta, filtered_contig.fasta.
If one or more are missing this subfolder is excluded. clonotype_id and consensus_id are suffixed with _cr for cellranger; entries from consensus.fasta becomes consensus_seq_cr.
...
Value
data frame (cl_long)
Close-your-eyes/igsc documentation built on Jan. 28, 2024, 10:28 p.m.
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View source: R/read_cellranger_outs.R
| read_cellranger_outs | R Documentation |
Read necessary file from 10X Genomics' cellranger output and return a concatenated data frame
Description
Caution: This function will add CDR3 sequences etc. uniformly to equal clonotype_ids even though if e.g. TRA was detected in every cell that has been assigned with clonotype_id i. Use read_cellranger_outs2 for a different behaviour, namely that this kind of imputation is not performed.
Usage
read_cellranger_outs(vdj_path)
Arguments
vdj_path |
path to the parent folder containing one or multiple subfolders with cellrangers VDJ outs |
Details
Required files in each subfolder of vdj_path are consensus_annotations.csv, filtered_contig_annotations.csv, consensus.fasta, concat_ref.fasta, filtered_contig.fasta. If one or more are missing this subfolder is excluded. clonotype_id and consensus_id are suffixed with _cr for cellranger; entries from consensus.fasta becomes consensus_seq_cr. ...
Value
data frame (cl_long)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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