@@ -1,11 +1,11 @@

 ^.*\.Rproj$

 ^\.Rproj\.user$

 extdata/.*\.json$

-^inst/script/*.csv

-^inst/script/*.json

-^inst/script/*.h5

+script/.*\.csv$

+script/.*\.json$

+script/.*\.h5$

 extdata/refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0/

-^doc$

+^docs$

 ^Meta$

 manuscript/

 ^_pkgdown\.yml$

@@ -13,4 +13,4 @@ manuscript/

 ^pkgdown$

 .ignore

 R/immcantation-utils.R

-^inst/WORDLIST

+^WORDLIST$

@@ -140,6 +140,7 @@ replace_cdb = function(x, name, value){

 #' @export

 #' @aliases ContigCellDB-mutate

 #' @examples

+#' data(ccdb_ex)

 #' ccdb_ex$contig_tbl

 #' ccdb_ex$cell_tbl

 #' ccdb_ex$cluster_tbl

@@ -150,6 +151,7 @@ setMethod("$", signature = c(x = 'ContigCellDB'), access_cdb)

 #' @export

 #'

 #' @examples

+#' data(ccdb_ex)

 #' ccdb_ex$contig_pk = c("sample","barcode","contig_id") # 'pop' is technically redundant with 'sample'

 #' # Take a subset of ccdb_ex

 #' ccdb_ex

@@ -106,6 +106,7 @@ cdhit = function(seqs, identity = NULL, kmerSize = NULL, min_length = 6, s = 1,

 ##' @export

 ##' @seealso [cdhit()]

 ##' @examples

+##' data(ccdb_ex)

 ##' res = cdhit_ccdb(ccdb_ex, 'cdr3_nt', type = 'DNA',

 ##' cluster_name = 'DNA97', identity = .965, min_length = 12, G = 1)

 ##' res$cluster_tbl

@@ -10,6 +10,7 @@ globalVariables('ngrp')

 #' @export

 #'

 #' @examples

+#' data(ccdb_ex)

 #' ccdb_ex = cluster_germline(ccdb_ex)

 #' ccdb_ex$cluster_tbl

 cluster_germline = function(ccdb, segment_keys = c('v_gene', 'j_gene', 'chain'), cluster_name = 'cluster_idx'){

@@ -13,6 +13,8 @@

 #'  3. `sample`: An artificial "replicate" from the original data defined by subsampling with replacement

 #'  4. `celltype`: The putative cell type of the contig.

 #'

+#' @name contigs_qc

+#' @usage data(contigs_qc)

 "contigs_qc"

 #' A preconstructed `ContigClusterDB` from the `contigs_qc` data

@@ -21,4 +23,6 @@

 #' \code{ccdb_ex = ContigCellDB_10XVDJ(contigs_qc, contig_pk = c('pop',   'sample', 'barcode', 'contig_id'), cell_pk = c('pop',   'sample', 'barcode'))}

 #' @seealso [contigs_qc]

 #'

+#' @name ccdb_ex

+#' @usage data(ccdb_ex)

 "ccdb_ex"

@@ -48,6 +48,7 @@ canonicalize_by_chain = function(tbl,  cell_identifiers = 'barcode', sort_factor

 #' @seealso [canonicalize_cluster()]

 #' @examples

 #' # Report beta chain with highest umi-count, breaking ties with reads

+#' data(ccdb_ex)

 #' beta = canonicalize_cell(ccdb_ex, chain == 'TRB',

 #' tie_break_keys = c('umis', 'reads'),

 #' contig_fields = c('umis', 'reads', 'chain', 'v_gene', 'd_gene', 'j_gene'))

@@ -1,4 +1,5 @@

 library(dplyr)

+data(ccdb_ex)

 ccdb_ex_small = ccdb_ex

 ccdb_ex_small$cell_tbl = ccdb_ex_small$cell_tbl[1:200,]

 ccdb_ex_small = cdhit_ccdb(ccdb_ex_small,

@@ -44,6 +44,7 @@ Fields in \code{contig_fields} will be copied over to the \code{cell_tbl}.

 }

 \examples{

 # Report beta chain with highest umi-count, breaking ties with reads

+data(ccdb_ex)

 beta = canonicalize_cell(ccdb_ex, chain == 'TRB',

 tie_break_keys = c('umis', 'reads'),

 contig_fields = c('umis', 'reads', 'chain', 'v_gene', 'd_gene', 'j_gene'))

@@ -46,6 +46,7 @@ Find a canonical contig to represent a cluster

 }

 \examples{

 library(dplyr)

+data(ccdb_ex)

 ccdb_ex_small = ccdb_ex

 ccdb_ex_small$cell_tbl = ccdb_ex_small$cell_tbl[1:200,]

 ccdb_ex_small = cdhit_ccdb(ccdb_ex_small,

@@ -24,9 +24,11 @@ Update or return a slot of \code{\link[=ContigCellDB]{ContigCellDB()}}

 Access public members of ContigCellDB object

 }

 \examples{

+data(ccdb_ex)

 ccdb_ex$contig_tbl

 ccdb_ex$cell_tbl

 ccdb_ex$cluster_tbl

+data(ccdb_ex)

 ccdb_ex$contig_pk = c("sample","barcode","contig_id") # 'pop' is technically redundant with 'sample'

 # Take a subset of ccdb_ex

 ccdb_ex

@@ -8,7 +8,7 @@

 \code{ccdb_ex = ContigCellDB_10XVDJ(contigs_qc, contig_pk = c('pop',   'sample', 'barcode', 'contig_id'), cell_pk = c('pop',   'sample', 'barcode'))}

 }

 \usage{

-ccdb_ex

+data(ccdb_ex)

 }

 \description{

 A preconstructed \code{ContigClusterDB} from the \code{contigs_qc} data

@@ -41,6 +41,7 @@ something smaller is passed.}

 Use \code{\link[=cdhit]{cdhit()}} to cluster a \code{\link[=ContigCellDB]{ContigCellDB()}}

 }

 \examples{

+data(ccdb_ex)

 res = cdhit_ccdb(ccdb_ex, 'cdr3_nt', type = 'DNA',

 cluster_name = 'DNA97', identity = .965, min_length = 12, G = 1)

 res$cluster_tbl

@@ -24,6 +24,7 @@ cluster_germline(

 Cluster contigs by germline properties

 }

 \examples{

+data(ccdb_ex)

 ccdb_ex = cluster_germline(ccdb_ex)

 ccdb_ex$cluster_tbl

 }

@@ -16,7 +16,7 @@ The following fields were defined ex post facto.

 }

 }

 \usage{

-contigs_qc

+data(contigs_qc)

 }

 \description{

 Data for c57bl6 and balbc mice TCR were downloaded from 10x Genomics website as

@@ -40,6 +40,7 @@ Perform additional clustering of sequences within groups

 }

 \examples{

 library(dplyr)

+data(ccdb_ex)

 ccdb_ex_small = ccdb_ex

 ccdb_ex_small$cell_tbl = ccdb_ex_small$cell_tbl[1:200,]

 ccdb_ex_small = cdhit_ccdb(ccdb_ex_small,