filterPDTMT.Rd
If inputLevel
is "Proteins", exclude features with
'Score.Sequest.HT.Sequest.HT' below minScore
,
'Number.of.Peptides' below minPeptides
, or identified as
'Contaminant' by ProteomeDiscoverer
.
If inputLevel
is "PeptideGroups", exclude features with
'Delta.Score.by.Search.Engine.Sequest.HT' below minDeltaScore
,
'Number.of.PSMs' below minPSMs
, or identified as
'Contaminant' by ProteomeDiscoverer
.
filterPDTMT(
sce,
inputLevel,
minScore = 0,
minPeptides = 0,
minDeltaScore = 0,
minPSMs = 0,
masterProteinsOnly = FALSE,
modificationsCol = "Modifications",
excludeUnmodifiedPeptides = FALSE,
keepModifications = NULL,
plotUpset = TRUE,
exclFile = NULL
)
A SummarizedExperiment
object (or a derivative).
Either "Proteins"
or "PeptideGroups"
,
indicating the type of features in sce
.
Numeric scalar, the minimum allowed value in the
'Score.Sequest.HT.Sequest.HT' column in order to retain the feature.
Only used if inputLevel
is "Proteins"
.
Numeric scalar, the minimum allowed value in the
'Number.of.Peptides' column in order to retain the feature.
Only used if inputLevel
is "Proteins"
.
Numeric scalar, the minimum allowed value in the
'Delta.Score.by.Search.Engine.Sequest.HT' column in order to retain the
feature. Only used if inputLevel
is "PeptideGroups"
.
Numeric scalar, the minimum allowed value in the
'Number.of.PSMs' column in order to retain the feature.
Only used if inputLevel
is "PeptideGroups"
.
Logical scalar indicating whether only master
proteins (where the Master
column value is
IsMasterProtein
) should be retained.
Character string pointing to a column containing
modification details. excludeUnmodifiedPeptides
and
keepModifications
will use information from this column. Only
used if inputLevel
is "PeptideGroups"
.
Logical scalar, whether to filter out
peptides without modifications. Only used if inputLevel
is
"PeptideGroups"
.
Character string (or NULL
) indicating
which modifications to retain in the analysis. Can be a regular
expression, which will be matched against the modificationsCol
.
If NULL
(the default), all rows are retained. Only used if
inputLevel
is "PeptideGroups"
.
Logical scalar, whether to generate an UpSet plot detailing the reasons for features being filtered out. Only generated if any feature is in fact filtered out.
Character scalar, the path to a text file where the
features that are filtered out are written. If NULL
(default),
excluded features are not recorded.
A filtered object of the same type as sce
.
## Proteins
sce <- importExperiment(
inFile = system.file("extdata", "pdtmt_example",
"Fig2_m23139_RTS_QC_varMods_Proteins.txt",
package = "einprot"),
iColPattern = "^Abundance.F.+.Sample.")$sce
dim(sce)
#> [1] 1723 16
sce <- filterPDTMT(sce = sce, inputLevel = "Proteins", minScore = 2,
minPeptides = 2, plotUpset = TRUE)
dim(sce)
#> [1] 1087 16
## PeptideGroups
sce <- importExperiment(
inFile = system.file("extdata", "pdtmt_example",
"Fig2_m23139_RTS_QC_varMods_PeptideGroups.txt",
package = "einprot"),
iColPattern = "^Abundance.F.+.Sample.")$sce
dim(sce)
#> [1] 5756 16
sce <- filterPDTMT(sce = sce, inputLevel = "PeptideGroups",
minPSMs = 2, plotUpset = TRUE, minDeltaScore = 0.2,
modificationsCol = "Modifications.in.Master.Proteins",
excludeUnmodifiedPeptides = TRUE)
dim(sce)
#> [1] 641 16