...
|
...
|
@@ -29,7 +29,7 @@
|
29
|
29
|
guessed_file_types
|
30
|
30
|
}
|
31
|
31
|
|
32
|
|
-# TODO: Choose between utils::read.delim(), readr::read_tsv(), and
|
|
32
|
+# TODO: (long term) Choose between utils::read.delim(), readr::read_tsv(), and
|
33
|
33
|
# data.table::fread() based on 'file'. If plain text, use fread(). If a
|
34
|
34
|
# compressed file, use readr::read_tsv() if available, otherwise
|
35
|
35
|
# utils::read_delim(). Longer term, combine data.table::fread() with
|
...
|
...
|
@@ -41,8 +41,8 @@
|
41
|
41
|
# utils::read.delim() when reading a gzipped file, albeit it with ~1.6-2x
|
42
|
42
|
# more total memory allocated. Therefore, there may be times users prefer
|
43
|
43
|
# to trade off faster speed for lower memory usage.
|
44
|
|
-# TODO: Formalise these benchmarks as a document in the bsseq package so that
|
45
|
|
-# we can readily re-visit these as needed.
|
|
44
|
+# TODO: (long term) Formalise these benchmarks as a document in the bsseq
|
|
45
|
+# package so that we can readily re-visit these as needed.
|
46
|
46
|
.readBismarkAsDT <- function(file,
|
47
|
47
|
col_spec = c("all", "BSseq", "GRanges"),
|
48
|
48
|
check = FALSE,
|
...
|
...
|
@@ -348,7 +348,6 @@
|
348
|
348
|
|
349
|
349
|
# Exported functions -----------------------------------------------------------
|
350
|
350
|
|
351
|
|
-# TODO: Support BPREDO?
|
352
|
351
|
# TODO: Support passing a colData so that metadata is automatically added to
|
353
|
352
|
# samples?
|
354
|
353
|
# TODO: Document that `...` are used to pass filepath, chunkdim, level, etc. to
|