... | ... |
@@ -1,11 +1,11 @@ |
1 | 1 |
^.*\.Rproj$ |
2 | 2 |
^\.Rproj\.user$ |
3 | 3 |
extdata/.*\.json$ |
4 |
-^inst/script/*.csv |
|
5 |
-^inst/script/*.json |
|
6 |
-^inst/script/*.h5 |
|
4 |
+script/.*\.csv$ |
|
5 |
+script/.*\.json$ |
|
6 |
+script/.*\.h5$ |
|
7 | 7 |
extdata/refdata-cellranger-vdj-GRCh38-alts-ensembl-2.0.0/ |
8 |
-^doc$ |
|
8 |
+^docs$ |
|
9 | 9 |
^Meta$ |
10 | 10 |
manuscript/ |
11 | 11 |
^_pkgdown\.yml$ |
... | ... |
@@ -13,4 +13,4 @@ manuscript/ |
13 | 13 |
^pkgdown$ |
14 | 14 |
.ignore |
15 | 15 |
R/immcantation-utils.R |
16 |
-^inst/WORDLIST |
|
16 |
+^WORDLIST$ |
... | ... |
@@ -140,6 +140,7 @@ replace_cdb = function(x, name, value){ |
140 | 140 |
#' @export |
141 | 141 |
#' @aliases ContigCellDB-mutate |
142 | 142 |
#' @examples |
143 |
+#' data(ccdb_ex) |
|
143 | 144 |
#' ccdb_ex$contig_tbl |
144 | 145 |
#' ccdb_ex$cell_tbl |
145 | 146 |
#' ccdb_ex$cluster_tbl |
... | ... |
@@ -150,6 +151,7 @@ setMethod("$", signature = c(x = 'ContigCellDB'), access_cdb) |
150 | 151 |
#' @export |
151 | 152 |
#' |
152 | 153 |
#' @examples |
154 |
+#' data(ccdb_ex) |
|
153 | 155 |
#' ccdb_ex$contig_pk = c("sample","barcode","contig_id") # 'pop' is technically redundant with 'sample' |
154 | 156 |
#' # Take a subset of ccdb_ex |
155 | 157 |
#' ccdb_ex |
... | ... |
@@ -106,6 +106,7 @@ cdhit = function(seqs, identity = NULL, kmerSize = NULL, min_length = 6, s = 1, |
106 | 106 |
##' @export |
107 | 107 |
##' @seealso [cdhit()] |
108 | 108 |
##' @examples |
109 |
+##' data(ccdb_ex) |
|
109 | 110 |
##' res = cdhit_ccdb(ccdb_ex, 'cdr3_nt', type = 'DNA', |
110 | 111 |
##' cluster_name = 'DNA97', identity = .965, min_length = 12, G = 1) |
111 | 112 |
##' res$cluster_tbl |
... | ... |
@@ -10,6 +10,7 @@ globalVariables('ngrp') |
10 | 10 |
#' @export |
11 | 11 |
#' |
12 | 12 |
#' @examples |
13 |
+#' data(ccdb_ex) |
|
13 | 14 |
#' ccdb_ex = cluster_germline(ccdb_ex) |
14 | 15 |
#' ccdb_ex$cluster_tbl |
15 | 16 |
cluster_germline = function(ccdb, segment_keys = c('v_gene', 'j_gene', 'chain'), cluster_name = 'cluster_idx'){ |
... | ... |
@@ -13,6 +13,8 @@ |
13 | 13 |
#' 3. `sample`: An artificial "replicate" from the original data defined by subsampling with replacement |
14 | 14 |
#' 4. `celltype`: The putative cell type of the contig. |
15 | 15 |
#' |
16 |
+#' @name contigs_qc |
|
17 |
+#' @usage data(contigs_qc) |
|
16 | 18 |
"contigs_qc" |
17 | 19 |
|
18 | 20 |
#' A preconstructed `ContigClusterDB` from the `contigs_qc` data |
... | ... |
@@ -21,4 +23,6 @@ |
21 | 23 |
#' \code{ccdb_ex = ContigCellDB_10XVDJ(contigs_qc, contig_pk = c('pop', 'sample', 'barcode', 'contig_id'), cell_pk = c('pop', 'sample', 'barcode'))} |
22 | 24 |
#' @seealso [contigs_qc] |
23 | 25 |
#' |
26 |
+#' @name ccdb_ex |
|
27 |
+#' @usage data(ccdb_ex) |
|
24 | 28 |
"ccdb_ex" |
... | ... |
@@ -48,6 +48,7 @@ canonicalize_by_chain = function(tbl, cell_identifiers = 'barcode', sort_factor |
48 | 48 |
#' @seealso [canonicalize_cluster()] |
49 | 49 |
#' @examples |
50 | 50 |
#' # Report beta chain with highest umi-count, breaking ties with reads |
51 |
+#' data(ccdb_ex) |
|
51 | 52 |
#' beta = canonicalize_cell(ccdb_ex, chain == 'TRB', |
52 | 53 |
#' tie_break_keys = c('umis', 'reads'), |
53 | 54 |
#' contig_fields = c('umis', 'reads', 'chain', 'v_gene', 'd_gene', 'j_gene')) |
... | ... |
@@ -44,6 +44,7 @@ Fields in \code{contig_fields} will be copied over to the \code{cell_tbl}. |
44 | 44 |
} |
45 | 45 |
\examples{ |
46 | 46 |
# Report beta chain with highest umi-count, breaking ties with reads |
47 |
+data(ccdb_ex) |
|
47 | 48 |
beta = canonicalize_cell(ccdb_ex, chain == 'TRB', |
48 | 49 |
tie_break_keys = c('umis', 'reads'), |
49 | 50 |
contig_fields = c('umis', 'reads', 'chain', 'v_gene', 'd_gene', 'j_gene')) |
... | ... |
@@ -24,9 +24,11 @@ Update or return a slot of \code{\link[=ContigCellDB]{ContigCellDB()}} |
24 | 24 |
Access public members of ContigCellDB object |
25 | 25 |
} |
26 | 26 |
\examples{ |
27 |
+data(ccdb_ex) |
|
27 | 28 |
ccdb_ex$contig_tbl |
28 | 29 |
ccdb_ex$cell_tbl |
29 | 30 |
ccdb_ex$cluster_tbl |
31 |
+data(ccdb_ex) |
|
30 | 32 |
ccdb_ex$contig_pk = c("sample","barcode","contig_id") # 'pop' is technically redundant with 'sample' |
31 | 33 |
# Take a subset of ccdb_ex |
32 | 34 |
ccdb_ex |
... | ... |
@@ -8,7 +8,7 @@ |
8 | 8 |
\code{ccdb_ex = ContigCellDB_10XVDJ(contigs_qc, contig_pk = c('pop', 'sample', 'barcode', 'contig_id'), cell_pk = c('pop', 'sample', 'barcode'))} |
9 | 9 |
} |
10 | 10 |
\usage{ |
11 |
-ccdb_ex |
|
11 |
+data(ccdb_ex) |
|
12 | 12 |
} |
13 | 13 |
\description{ |
14 | 14 |
A preconstructed \code{ContigClusterDB} from the \code{contigs_qc} data |
... | ... |
@@ -41,6 +41,7 @@ something smaller is passed.} |
41 | 41 |
Use \code{\link[=cdhit]{cdhit()}} to cluster a \code{\link[=ContigCellDB]{ContigCellDB()}} |
42 | 42 |
} |
43 | 43 |
\examples{ |
44 |
+data(ccdb_ex) |
|
44 | 45 |
res = cdhit_ccdb(ccdb_ex, 'cdr3_nt', type = 'DNA', |
45 | 46 |
cluster_name = 'DNA97', identity = .965, min_length = 12, G = 1) |
46 | 47 |
res$cluster_tbl |