| msFilter {MSPrep} | R Documentation |
Filters compounds to those found in specified proportion of samples.
msFilter(
data,
filterPercent = 0.8,
compVars = c("mz", "rt"),
sampleVars = c("subject_id"),
colExtraText = NULL,
separator = NULL,
missingValue = NA,
returnToSE = FALSE,
returnToDF = FALSE
)
data |
Data set as either a data frame or 'SummarizedExperiement'. |
filterPercent |
Decimal value indicating filtration threshold. Compounds which are present in fewer samples than the specified proportion will be removed. |
compVars |
Vector of the columns which identify compounds. If a 'SummarizedExperiment' is used for 'data', row variables will be used. |
sampleVars |
Vector of the ordered sample variables found in each sample column. |
colExtraText |
Any extra text to ignore at the beginning of the sample columns names. Unused for 'SummarizedExperiments'. |
separator |
Character or text separating each sample variable in sample columns. Unused for 'SummarizedExperiment'. |
missingValue |
Specifies the abundance value which indicates missing data. May be a numeric or 'NA'. |
returnToSE |
Logical value indicating whether to return as 'SummarizedExperiment' |
returnToDF |
Logical value indicating whether to return as data frame. |
A data frame or 'SummarizedExperiment' with filtered abundance data. Default return type is set to match the data input but may be altered with the 'returnToSE' or 'returnToDF' arguments.
# Load example data set, summarize replicates
data(msquant)
summarizedDF <- msSummarize(msquant,
compVars = c("mz", "rt"),
sampleVars = c("spike", "batch", "replicate",
"subject_id"),
cvMax = 0.50,
minPropPresent = 1/3,
colExtraText = "Neutral_Operator_Dif_Pos_",
separator = "_",
missingValue = 1)
# Filter the dataset using a 80% filter rate
filteredDF <- msFilter(summarizedDF,
filterPercent = 0.8,
compVars = c("mz", "rt"),
sampleVars = c("spike", "batch", "subject_id"),
separator = "_")