diff --git a/R/converters_DIANNtoMSstatsFormat.R b/R/converters_DIANNtoMSstatsFormat.R index 3205aca9..1b46976b 100644 --- a/R/converters_DIANNtoMSstatsFormat.R +++ b/R/converters_DIANNtoMSstatsFormat.R @@ -15,7 +15,7 @@ #' column, i.e. the global q-value for the protein group. If MBR is true, the #' qvalue cutoff for the Lib.PG.Q.Value column, i.e. the protein group q-value for #' the library created after the first MBR pass. Default is 0.01. -#' @param useUniquePeptide should unique pepties be removed +#' @param useUniquePeptide should unique peptides be removed #' @param removeFewMeasurements should proteins with few measurements be removed #' @param removeOxidationMpeptides should peptides with oxidation be removed #' @param removeProtein_with1Feature should proteins with a single feature be removed diff --git a/man/DIANNtoMSstatsFormat.Rd b/man/DIANNtoMSstatsFormat.Rd index 76467174..2ea6e068 100644 --- a/man/DIANNtoMSstatsFormat.Rd +++ b/man/DIANNtoMSstatsFormat.Rd @@ -42,7 +42,7 @@ column, i.e. the global q-value for the protein group. If MBR is true, the qvalue cutoff for the Lib.PG.Q.Value column, i.e. the protein group q-value for the library created after the first MBR pass. Default is 0.01.} -\item{useUniquePeptide}{should unique pepties be removed} +\item{useUniquePeptide}{should unique peptides be removed} \item{removeFewMeasurements}{should proteins with few measurements be removed} diff --git a/man/MSstatsConvert.Rd b/man/MSstatsConvert.Rd index 387e6ff6..e8714296 100644 --- a/man/MSstatsConvert.Rd +++ b/man/MSstatsConvert.Rd @@ -19,12 +19,12 @@ signal processing tools to a format suitable for statistical analysis with the M } \author{ -\strong{Maintainer}: Mateusz Staniak \email{mtst@mstaniak.pl} +\strong{Maintainer}: Anthony Wu \email{wu.anthon@northeastern.edu} Authors: \itemize{ + \item Mateusz Staniak \email{mtst@mstaniak.pl} \item Devon Kohler \email{kohler.d@northeastern.edu} - \item Anthony Wu \email{wu.anthon@northeastern.edu} \item Meena Choi \email{mnchoi67@gmail.com} \item Ting Huang \email{thuang0703@gmail.com} \item Olga Vitek \email{o.vitek@northeastern.edu} diff --git a/man/SpectronauttoMSstatsFormat.Rd b/man/SpectronauttoMSstatsFormat.Rd index 30956a78..36ef3f85 100644 --- a/man/SpectronauttoMSstatsFormat.Rd +++ b/man/SpectronauttoMSstatsFormat.Rd @@ -7,7 +7,7 @@ SpectronauttoMSstatsFormat( input, annotation = NULL, - intensity = "PeakArea", + intensity = c("PeakArea", "NormalizedPeakArea", "MS1Quantity"), excludedFromQuantificationFilter = TRUE, filter_with_Qvalue = FALSE, qvalue_cutoff = 0.01,