From 7bec8306e5e05e5f2943e129b8fce4dba79fc35e Mon Sep 17 00:00:00 2001 From: David Mayer Date: Wed, 1 Oct 2025 20:07:41 +0000 Subject: [PATCH] run devtools::document() to update any .Rd files that need it --- DESCRIPTION | 2 +- man/calculateProcessRuntime.Rd | 2 +- man/cleanFAHeaders.Rd | 4 ++-- man/cleanString.Rd | 2 +- man/convertIPRScanDomainTable2FA.Rd | 2 +- man/createIPRScanDomainTable.Rd | 6 +++--- man/ensureUniqAccNum.Rd | 4 ++-- man/getDomainsFromFA.Rd | 6 +++--- man/getIPRScanColNames.Rd | 2 +- man/getProcessRuntimeWeights.Rd | 2 +- man/readIPRScanTSV.Rd | 2 +- man/writeProcessRuntime2TSV.Rd | 2 +- man/writeProcessRuntime2YML.Rd | 4 ++-- 13 files changed, 20 insertions(+), 20 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index eaf681d1..7e4708d8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,7 +27,7 @@ Depends: R (>= 4.4.0) Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 VignetteBuilder: knitr Imports: ape, diff --git a/man/calculateProcessRuntime.Rd b/man/calculateProcessRuntime.Rd index 579ea2b6..1027e39a 100644 --- a/man/calculateProcessRuntime.Rd +++ b/man/calculateProcessRuntime.Rd @@ -7,7 +7,7 @@ calculateProcessRuntime(dir_job_results) } \arguments{ -\item{dir_job_results}{\link{chr} path to MolEvolvR job_results +\item{dir_job_results}{\link[rlang:vector-construction]{rlang::chr} path to MolEvolvR job_results directory} } \value{ diff --git a/man/cleanFAHeaders.Rd b/man/cleanFAHeaders.Rd index e93d0ca3..b5dee51f 100644 --- a/man/cleanFAHeaders.Rd +++ b/man/cleanFAHeaders.Rd @@ -7,12 +7,12 @@ cleanFAHeaders(fasta) } \arguments{ -\item{fasta}{An \link{XStringSet} object representing the sequences from a +\item{fasta}{An \link[Biostrings:XStringSet-class]{Biostrings::XStringSet} object representing the sequences from a FASTA file. The sequence names (headers) will be adjusted for uniqueness and sanitized.} } \value{ -\link{XStringSet} fasta with adjusted names (headers) +\link[Biostrings:XStringSet-class]{Biostrings::XStringSet} fasta with adjusted names (headers) } \description{ Parse accesion numbers from fasta and add a diff --git a/man/cleanString.Rd b/man/cleanString.Rd index 0dc2937e..ffb55a46 100644 --- a/man/cleanString.Rd +++ b/man/cleanString.Rd @@ -10,7 +10,7 @@ cleanString(string) \item{string}{} } \value{ -\link{string} string with only alphanumerics, "_", "+", and "." +\link[rlang:string]{rlang::string} string with only alphanumerics, "_", "+", and "." } \description{ Keep only alphanumerics, "\emph{", "+", and "." in strings diff --git a/man/convertIPRScanDomainTable2FA.Rd b/man/convertIPRScanDomainTable2FA.Rd index 7b8b9d24..23396bfb 100644 --- a/man/convertIPRScanDomainTable2FA.Rd +++ b/man/convertIPRScanDomainTable2FA.Rd @@ -12,7 +12,7 @@ convertIPRScanDomainTable2FA(df_iprscan_domains) \item{df_iprscan_domains}{\link{tbl_df} return value from createIPRScanDomainTable} } \value{ -\link{AAStringSet} A domain fasta containing all the domains for a +\link[Biostrings:XStringSet-class]{Biostrings::AAStringSet} A domain fasta containing all the domains for a single protein in the original fasta passed as an argument to createIPRScanDomainTable() } \description{ diff --git a/man/createIPRScanDomainTable.Rd b/man/createIPRScanDomainTable.Rd index b5d4abf7..367eaafd 100644 --- a/man/createIPRScanDomainTable.Rd +++ b/man/createIPRScanDomainTable.Rd @@ -13,15 +13,15 @@ createIPRScanDomainTable( ) } \arguments{ -\item{accnum}{\link{chr} a \emph{single} accession number from the original fasta (fasta param) +\item{accnum}{\link[rlang:vector-construction]{rlang::chr} a \emph{single} accession number from the original fasta (fasta param) which will be used to search for its sequence's domains (df_iprscan param)} -\item{fasta}{\link{AAStringSet} original fasta file which was fed into interproscan} +\item{fasta}{\link[Biostrings:XStringSet-class]{Biostrings::AAStringSet} original fasta file which was fed into interproscan} \item{df_iprscan}{\link{tbl_df} the output TSV of interproscan, read as a tibble with readIPRScanTSV()} -\item{analysis}{\link{chr} the domain databases to extract sequences from} +\item{analysis}{\link[rlang:vector-construction]{rlang::chr} the domain databases to extract sequences from} } \value{ \link{tbl_df} table with each domain sequence and a new identifier column diff --git a/man/ensureUniqAccNum.Rd b/man/ensureUniqAccNum.Rd index ddb4a70d..cc236149 100644 --- a/man/ensureUniqAccNum.Rd +++ b/man/ensureUniqAccNum.Rd @@ -7,10 +7,10 @@ ensureUniqAccNum(accnums) } \arguments{ -\item{accnums}{\link{chr} a vector of accession numbers} +\item{accnums}{\link[rlang:vector-construction]{rlang::chr} a vector of accession numbers} } \value{ -\link{chr} a vector of adjusted, unique accession numbers +\link[rlang:vector-construction]{rlang::chr} a vector of adjusted, unique accession numbers } \description{ Append an index of occurence suffix to each accession number (or any diff --git a/man/getDomainsFromFA.Rd b/man/getDomainsFromFA.Rd index 08ff911d..1dab684a 100644 --- a/man/getDomainsFromFA.Rd +++ b/man/getDomainsFromFA.Rd @@ -12,14 +12,14 @@ getDomainsFromFA( ) } \arguments{ -\item{fasta}{\link{AAStringSet} a protein (AA) fasta} +\item{fasta}{\link[Biostrings:XStringSet-class]{Biostrings::AAStringSet} a protein (AA) fasta} \item{df_iprscan}{\link{tbl_df} the interproscan results from the original fasta} -\item{analysis}{\link{chr} the domain databases to extract sequences from} +\item{analysis}{\link[rlang:vector-construction]{rlang::chr} the domain databases to extract sequences from} } \value{ -fasta_domains \link{AAStringSet} fasta of domains +fasta_domains \link[Biostrings:XStringSet-class]{Biostrings::AAStringSet} fasta of domains } \description{ getDomainsFromFA diff --git a/man/getIPRScanColNames.Rd b/man/getIPRScanColNames.Rd index 7518081f..02268b6d 100644 --- a/man/getIPRScanColNames.Rd +++ b/man/getIPRScanColNames.Rd @@ -9,7 +9,7 @@ molevol_scripts/R/colnames_molevol.R)} getIPRScanColNames() } \value{ -\link{chr} interproscan column names used throughout molevolvr +\link[rlang:vector-construction]{rlang::chr} interproscan column names used throughout molevolvr } \description{ Constructor function for interproscan column names diff --git a/man/getProcessRuntimeWeights.Rd b/man/getProcessRuntimeWeights.Rd index de0e2ea6..2e7f1923 100644 --- a/man/getProcessRuntimeWeights.Rd +++ b/man/getProcessRuntimeWeights.Rd @@ -7,7 +7,7 @@ getProcessRuntimeWeights(medians_yml_path = NULL) } \arguments{ -\item{dir_job_results}{\link{chr} path to MolEvolvR job_results +\item{dir_job_results}{\link[rlang:vector-construction]{rlang::chr} path to MolEvolvR job_results directory} } \value{ diff --git a/man/readIPRScanTSV.Rd b/man/readIPRScanTSV.Rd index 0c646c48..ae3082b2 100644 --- a/man/readIPRScanTSV.Rd +++ b/man/readIPRScanTSV.Rd @@ -8,7 +8,7 @@ column names and types} readIPRScanTSV(filepath) } \arguments{ -\item{filepath}{\link{chr} path to interproscan output TSV} +\item{filepath}{\link[rlang:vector-construction]{rlang::chr} path to interproscan output TSV} } \value{ \link{tbl_df} interproscan output table diff --git a/man/writeProcessRuntime2TSV.Rd b/man/writeProcessRuntime2TSV.Rd index 0e045a5c..894417dc 100644 --- a/man/writeProcessRuntime2TSV.Rd +++ b/man/writeProcessRuntime2TSV.Rd @@ -7,7 +7,7 @@ writeProcessRuntime2TSV(dir_job_results, filepath) } \arguments{ -\item{dir_job_results}{\link{chr} path to MolEvolvR job_results} +\item{dir_job_results}{\link[rlang:vector-construction]{rlang::chr} path to MolEvolvR job_results} \item{filepath}{path to save tsv file} } diff --git a/man/writeProcessRuntime2YML.Rd b/man/writeProcessRuntime2YML.Rd index 5e0a05a4..c38e19d3 100644 --- a/man/writeProcessRuntime2YML.Rd +++ b/man/writeProcessRuntime2YML.Rd @@ -7,9 +7,9 @@ writeProcessRuntime2YML(dir_job_results, filepath = NULL) } \arguments{ -\item{dir_job_results}{\link{chr} path to MolEvolvR job_results directory} +\item{dir_job_results}{\link[rlang:vector-construction]{rlang::chr} path to MolEvolvR job_results directory} -\item{filepath}{\link{chr} path to save YAML file; if NULL, +\item{filepath}{\link[rlang:vector-construction]{rlang::chr} path to save YAML file; if NULL, uses ./molevol_scripts/log_data/job_proc_weights.yml} } \description{