A wrapper function for addPerCellQC. Calculate general quality control metrics for each cell in the count matrix.
runPerCellQC(
inSCE,
useAssay = "counts",
collectionName = NULL,
geneSetList = NULL,
geneSetListLocation = "rownames",
geneSetCollection = NULL,
mitoRef = NULL,
mitoIDType = NULL,
mitoPrefix = NULL,
mitoID = NULL,
mitoGeneLocation = NULL,
percent_top = c(50, 100, 200, 500),
use_altexps = FALSE,
flatten = TRUE,
detectionLimit = 0,
BPPARAM = BiocParallel::SerialParam()
)
A SingleCellExperiment object.
A string specifying which assay in the SCE to use. Default
"counts"
.
Character. Name of a GeneSetCollection
obtained
by using one of the importGeneSet*
functions. Default NULL
.
List of gene sets to be quantified. The genes in the
assays will be matched to the genes in the list based on
geneSetListLocation
. Default NULL
.
Character or numeric vector. If set to
'rownames'
, then the genes in geneSetList
will be looked up in
rownames(inSCE)
. If another character is supplied, then genes will be
looked up in the column names of rowData(inSCE)
. A character vector
with the same length as geneSetList
can be supplied if the IDs for
different gene sets are found in different places, including a mixture of
'rownames'
and rowData(inSCE)
. An integer or integer vector can
be supplied to denote the column index in rowData(inSCE)
. Default
'rownames'
.
Class of GeneSetCollection
from package
GSEABase. The location of the gene IDs in inSCE
should be in the
description
slot of each gene set and should follow the
same notation as geneSetListLocation
. The function
getGmt
can be used to read in gene sets from a GMT
file. If reading a GMT file, the second column for each gene set should be
the description denoting the location of the gene IDs in inSCE
. These
gene sets will be included with those from geneSetList
if both
parameters are provided.
Character. The species used to extract mitochondrial genes ID
from build-in mitochondrial geneset in SCTK. Available species options are
"human"
and "mouse"
. Default is NULL
.
Character. Types of mitochondrial gene id. SCTK supports
"symbol"
, "entrez"
, "ensembl"
and
"ensemblTranscriptID"
. It is used with mitoRef
to extract
mitochondrial genes from build-in mitochondrial geneset in SCTK. Default
NULL
.
Character. The prefix used to get mitochondrial gene from
either rownames(inSCE)
or columns of rowData(inSCE)
specified
by mitoGeneLocation
. This parameter is usually used to extract mito
genes from gene symbol. For example, mitoPrefix = "^MT-"
can be used
to detect mito gene symbols like "MT-ND4".
Character. A vector of mitochondrial genes to be quantified.
Character. Describes the location within inSCE
where the gene identifiers in the mitochondrial gene sets should be mapped.
If set to "rownames"
then the features will be searched for among
rownames(inSCE)
. This can also be set to one of the column names of
rowData(inSCE)
in which case the gene identifies will be mapped to
that column in the rowData
of inSCE
. See
featureIndex
for more information. Default NULL
.
An integer vector. Each element is treated as a number of
top genes to compute the percentage of library size occupied by the most
highly expressed genes in each cell. Default c(50, 100, 200, 500)
.
Logical scalar indicating whether QC statistics should
be computed for alternative Experiments in inSCE
(altExps(inSCE)
). If TRUE
, statistics are computed for all
alternative experiments. Alternatively, an integer or character vector
specifying the alternative Experiments to use to compute QC statistics.
Alternatively NULL
, in which case alternative experiments are not
used. Default FALSE
.
Logical scalar indicating whether the nested
DataFrame-class in the output should be flattened. Default
TRUE
.
A numeric scalar specifying the lower detection limit
for expression. Default 0
A BiocParallelParam object specifying whether the QC
calculations should be parallelized. Default
BiocParallel::SerialParam()
.
A SingleCellExperiment object with
cell QC metrics added to the colData slot. If geneSetList
or
geneSetCollection
are provided, then the rownames for each gene set
will be saved in metadata(inSCE)$sctk$runPerCellQC[[sample]]$geneSets
.
This function allows multiple ways to import mitochondrial genes and quantify their expression.
Using mitoRef
, mitoIDType
and mitoGeneLocation
parameters will load the build-in mitochondrial geneset in SCTK package.
Using mitoPrefix
and mitoGeneLocation
parameters will
extract mitochondrial genes from either rownames(inSCE) or columns of
rowData(inSCE) specified ny parameter mitoGeneLocation
Using mitoID
and mitoGeneLocation
parameters will
quantify the expression of mitochondrial genes stored in mitoID
.
mitoGeneLocation
is required if you use any methods mentioned above to
quantify mitochondrial gene expression. Please make sure
mitoGeneLocation
is pointing to the location within inSCE object that
stores the correct mitochondrial genes ID.
addPerCellQC
,
link{plotRunPerCellQCResults}
, runCellQC