A Comprehensive Toolbox for Gene Expression Deconvolution


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Documentation for package ‘CellMix’ version 1.6.2

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A B C D E F G H I K L M N O P Q R S T U V W misc

CellMix-package Gene Expression Deconvolution

-- A --

Abbas Basis Matrix for Whole Blood Expression Deconvolution
Abbas-markers Optimised Set of Marker Genes for Immune Cells
addNames Generating Names
annotation Accessing Data in Marker Lists
annotation-method Accessing Data in Marker Lists
annotation-methods Accessing Data in Marker Lists
annotation<- Accessing Data in Marker Lists
annotation<--method Accessing Data in Marker Lists
annotation<--methods Accessing Data in Marker Lists
anyRequired Checking Input and Output Data for GED Algorithms
applyBy Group Apply
applyBy.ExpressionSet Group Apply
applyBy.matrix Group Apply
asCBC Blood Sample Deconvolution
asCBC-method Blood Sample Deconvolution
asCBC-methods Blood Sample Deconvolution
asGeneIdentifierType Utility function for Biological Identifiers
attachMarkers Class for Marker Gene Lists

-- B --

barplot.MarkerList Plotting MarkerList Objects
basis-method Accessing Data from CellMix Dataset
basisfit Accessing Fit Data in Deconvolution Results
basismarkermap Heatmaps Highlighting Markers
beeswarm.MarkerList Plotting Markers
bioc2gpl Mapping Bioconductor Annotation packages to GEO GPL Identifiers
biocann_map Retrieving ID Conversion Maps
biocann_mapname Annotation Tools
biocann_object Retrieving Bioconductor Annotation Maps
biocann_pkgname Annotation Tools
biocann_pkgobject Annotation Tools
boxplotBy Split Boxplot by Group
boxplotBy.default Split Boxplot by Group
boxplotBy.NMF Split Boxplot by Group

-- C --

cbind.ExpressionSet Combining Expression Matrices
cellMarkers Loading Marker Lists from Registry
cellMarkersInfo Loading Marker Lists from Registry
CellMix Gene Expression Deconvolution
cellmix.getOption Package Specific Options for CellMix
cellmix.options Package Specific Options for CellMix
cellmix.printOptions Package Specific Options for CellMix
cellmix.resetOptions Package Specific Options for CellMix
checkConstraints Checking Linear Constraints
checkS4 Validity Functions of Registry Fields
coef-method Accessing Data from CellMix Dataset
coeffit Accessing Fit Data in Deconvolution Results
colApplyBy Group Apply
colMaxsBy Group Apply
colMeansBy Group Apply
colMediansBy Group Apply
colMinsBy Group Apply
colSumsBy Group Apply
combine-method Combine markers from multiple cell types of a MarkerList object, based on groups defined by a given factor.
Compare-method Operations on MarkerList Objects
connectivity Accessing Data in Marker Lists
connectivity-method Accessing Data in Marker Lists
connectivity-methods Accessing Data in Marker Lists
convertIDs Converting Gene or Probeset IDs
convertIDs-method Converting Gene or Probeset IDs
convertIDs-methods Converting Gene or Probeset IDs
cs-lsfit-ged Cell-Specific Expression by Standard Least-Squares
cs-qprog-ged Partial Gene Expression Deconvolution by Quadratic Programming
csplot Plots Cell-Specific FDR Estimates
csplot.character Plots Cell-Specific FDR Estimates
csplot.csSAM Partial Gene Expression Deconvolution with csSAM
csplot.NMFfit Plots Cell-Specific FDR Estimates
csplot.NMFfitX Plots Cell-Specific FDR Estimates
csSAM-ged Partial Gene Expression Deconvolution with csSAM
csTopTable Compute Cell-Specific Statistics
csTopTable.array Compute Cell-Specific Statistics
csTopTable.character Compute Cell-Specific Statistics
csTopTable.csSAM Partial Gene Expression Deconvolution with csSAM
csTopTable.DSection Partial Gene Expression Deconvolution with DSection
csTopTable.matrix Compute Cell-Specific Statistics
csTopTable.NMFfit Compute Cell-Specific Statistics
csTopTable.NMFfitX Compute Cell-Specific Statistics

-- D --

DataSource Gene Expression Data Sources
deconf-ged Complete Gene Expression Deconvolution: Method deconf
details Accessing Data in Marker Lists
details-method Accessing Data in Marker Lists
details-methods Accessing Data in Marker Lists
dim-method Dimensions in ExpressionMix Objects
dimnames-method Dimensions in ExpressionMix Objects
dimnames<--method Dimensions in ExpressionMix Objects
dims-method Accessing Data from CellMix Dataset
drop-method Utility Functions for MarkerList Objects
dropvalues Utility Functions for MarkerList Objects
DSA-ged Complete Deconvolution using Digital Sorting Algorithm (DSA)
DSAproportions Digital Sorting Algorithm: Proportion Estimation Method
DSection DSection Gene Expression Deconvolution Method
DSection-ged Partial Gene Expression Deconvolution with DSection

-- E --

enforceMarkers Enforcing Marker Block Patterns
enforceMarkers-method Enforcing Marker Block Patterns
enforceMarkers-methods Enforcing Marker Block Patterns
eset Extracting Expression Data
eset-method Extracting Expression Data
eset-methods Extracting Expression Data
exp-method Numeric Computations on ExpressionSet objects
expb Numeric Computations on ExpressionSet objects
expb-method Numeric Computations on ExpressionSet objects
expb-methods Numeric Computations on ExpressionSet objects
ExpressionMix Factory Method for ExpressionMix Objects
ExpressionMix-class Class for Gene Expression Deconvolution Benchmark Datasets
ExpressionMix-method Factory Method for ExpressionMix Objects
ExpressionMix-methods Factory Method for ExpressionMix Objects
ExpressionMix-subset Subsetting ExpressionMix Objects
exprs Extracting Feature Names
exprs-method Extracting Feature Names
exprs-method Accessing Data from CellMix Dataset
exprs-methods Extracting Feature Names
extractMarkers Extract Markers from Pure Samples.
extractMarkers-method Extract Markers from Pure Samples.
extractMarkers-methods Extract Markers from Pure Samples.

-- F --

featureNames Extracting Feature Names
featureNames-method Extracting Feature Names
featureNames-methods Extracting Feature Names
featureNames<- Extracting Feature Names
featureNames<--method Dimensions in ExpressionMix Objects
featureNames<--methods Extracting Feature Names
fetchData Fetching Data from Data Sources
flatten Flattening Marker Lists
flatten-method Flattening Marker Lists
flatten-methods Flattening Marker Lists

-- G --

gCBC Blood Sample Deconvolution
ged Main Interface for Gene Expression Deconvolution Methods
ged-method Main Interface for Gene Expression Deconvolution Methods
ged-methods Main Interface for Gene Expression Deconvolution Methods
gedAlgorithm Managing Gene Expression Deconvolution Algorithms
gedAlgorithm.csSAM Partial Gene Expression Deconvolution with csSAM
gedAlgorithm.cs_lsfit Cell-Specific Expression by Standard Least-Squares
gedAlgorithm.cs_qprog Partial Gene Expression Deconvolution by Quadratic Programming
gedAlgorithm.deconf Complete Gene Expression Deconvolution: Method deconf
gedAlgorithm.DSA Complete Deconvolution using Digital Sorting Algorithm (DSA)
gedAlgorithm.DSection Partial Gene Expression Deconvolution with DSection
gedAlgorithm.lsfit Partial Gene Expression Deconvolution by Standard Least-Squares
gedAlgorithm.meanProfile Partial Gene Expression Deconvolution: Marker Mean Expression Profile
gedAlgorithm.qprog Partial Gene Expression Deconvolution by Quadratic Programming
gedAlgorithm.ssFrobenius Complete Gene Expression Deconvolution by Semi-Supervised NMF
gedAlgorithm.ssKL Complete Gene Expression Deconvolution by Semi-Supervised NMF
gedAlgorithmInfo Managing Gene Expression Deconvolution Algorithms
gedBlood Blood Sample Deconvolution
gedCheck Checking a Deconvolution Method
gedData Loading Gene Expression Deconvolution Data
GEDdata-access Accessing Data from CellMix Dataset
gedDataInfo Loading Gene Expression Deconvolution Data
GEDdownload Downloading Gene Expression Deconvolution Datasets
gedInput Checking Input and Output Data for GED Algorithms
gedIO Checking Input and Output Data for GED Algorithms
gedOutput Checking Input and Output Data for GED Algorithms
gedProportions Estimating Cell Proportions from Known Signatures
GEDStrategy Factory Methods for GEDStrategy Objects
GEDStrategy-class Class for GED Algorithms
GEDStrategy-method Factory Methods for GEDStrategy Objects
GEDStrategy-methods Factory Methods for GEDStrategy Objects
geneIds Accessing Data in Marker Lists
geneIds-method Accessing Data in Marker Lists
geneIds-methods Accessing Data in Marker Lists
geneIds<- Accessing Data in Marker Lists
geneIds<--method Accessing Data in Marker Lists
geneIds<--methods Accessing Data in Marker Lists
geneIdType Accessing Data in Marker Lists
geneIdType-method Accessing Data in Marker Lists
geneIdType-methods Accessing Data in Marker Lists
geneIdType<- Accessing Data in Marker Lists
geneIdType<--method Accessing Data in Marker Lists
geneIdType<--methods Accessing Data in Marker Lists
geneValues Accessing Data in Marker Lists
geneValues-method Accessing Data in Marker Lists
geneValues-methods Accessing Data in Marker Lists
geneValues<- Accessing Data in Marker Lists
geneValues<--methods Accessing Data in Marker Lists
getAnnotation Extracting Annotation from Objects
getGSE Downloading GSE Datasets from GEO
getMarkers Class for Marker Gene Lists
gMarkerList Generating Marker Lists
gmarkers Generating Marker Lists
GPL2bioc Map Between Bioconductor Annotation Packages and GEO GPL Identifiers
gpl2bioc Mapping Bioconductor Annotation packages to GEO GPL Identifiers
Grigoryev-markers Grigoryev - Cytometry Antigen Markers
GSE11058_pdata Cell Line Proportions for Dataset GSE11058
GSE20300_pdata Complete Blood Count for Dataset GSE20300
GSE3649_fdata Feature Annotation Data for Dataset GSE3649
GSE3649_pdata Phenotypic Annotation Data for Dataset GSE3649

-- H --

HaemAtlas HaemAtlas Dataset - Immune Cells
HaemAtlas-markers HaemAtlas Marker List for Immune Cells - Watkins et al. (2009)
has.markers Class for Marker Gene Lists
hasAnnotation Extracting Annotation from Objects
hasDuplicated Utility Functions for MarkerList Objects
hasValues Accessing Data in Marker Lists
hist.MarkerList Plotting Markers

-- I --

idFilter Gene Identifier Filtering Strategies
idFilterAffy Gene Identifier Filtering Strategies
idFilterAll Gene Identifier Filtering Strategies
idFilterAuto Gene Identifier Filtering Strategies
idFilterFirstN Gene Identifier Filtering Strategies
idFilterInjective Gene Identifier Filtering Strategies
idFilterMAuto Gene Identifier Filtering Strategies
idFilterOneToMany Gene Identifier Filtering Strategies
idFilterOneToOne Gene Identifier Filtering Strategies
idtype Identifying Gene or Probe ID Type
idtype-method Identifying Gene or Probe ID Type
idtype-methods Identifying Gene or Probe ID Type
incidence Accessing Data in Marker Lists
incidence-method Accessing Data in Marker Lists
incidence-methods Accessing Data in Marker Lists
initialize-method Initialize method for ExpressionMix object
intersect Enhanced Subsetting for Matrix-like Data
intersect-method Enhanced Subsetting for Matrix-like Data
IRIS Immune Response In-Silico (IRIS) Data
IRIS-markers Marker Genes for Immune Cells (IRIS)
is.anndb Annotation Tools
is.annpkg Annotation Tools
is.idtype Utility function for Biological Identifiers
is.probeid Utility function for Biological Identifiers
is.probetype Utility function for Biological Identifiers
isDataSource Gene Expression Data Sources
isMarkerList Class for Marker Gene Lists
isRequired Checking Input and Output Data for GED Algorithms
is_logscale Detect Log-transformed Data

-- K --

kappa.MarkerList Condition Number of a Marker List

-- L --

log-method Numeric Computations on ExpressionSet objects
log_transform Detect Log-transformed Data
lpure Acessing Pure or Mixed Sample Data
lsfit-ged Partial Gene Expression Deconvolution by Standard Least-Squares

-- M --

mapIdentifiers-method Converting Gene or Probeset IDs
mapIDs Mapping Gene Identifiers
MarkerList Factory Method for Marker Lists
MarkerList-class Class for Marker Gene Lists
MarkerList-method Factory Method for Marker Lists
MarkerList-methods Factory Method for Marker Lists
markermap Heatmaps Highlighting Markers
markermap-method Heatmaps Highlighting Markers
markermap-methods Heatmaps Highlighting Markers
markerScoreAbbas Marker Scoring Method: Abbas et al. (2009)
markerScoreHSD Marker Scoring Method: Tukey Honest Significant Difference
markerScoreMaxcol Marker scoring method: Max Expression
markerScoreMethod Extract Markers from Pure Samples.
markerScoreScorem Marker scoring method: SCOREM
MarkerSetCollection Factory Methods for Marker Gene Set Collections
MarkerSetCollection-class Classes for Marker Gene Set Collections
MarkerSetCollection-methods Factory Methods for Marker Gene Set Collections
markersGrigoryev Cytometry Antigen Expression from Grigoryev et al. (2010)
marknames Accessing Data in Marker Lists
marknames-method Accessing Data in Marker Lists
marknames-methods Accessing Data in Marker Lists
match.cell Assigning Estimated Signature to Real Cell-Types
match.nmf Assigning Estimated Signature to Real Cell-Types
matchIndex Creating Mapping from Marker Lists
matchIndex-method Creating Mapping from Marker Lists
matchIndex-methods Creating Mapping from Marker Lists
match_first Returns the index of the first match in a reference table
meanProfile-ged Partial Gene Expression Deconvolution: Marker Mean Expression Profile
mergeList Merge two lists
mixData Extracting Mixture Data
mixData-method Extracting Mixture Data
mixData-methods Extracting Mixture Data
mixData<- Extracting Mixture Data
mixData<--method Extracting Mixture Data
mixData<--methods Extracting Mixture Data
mixedSamples Acessing Pure or Mixed Sample Data
mlsei Multivariate Least Squares with Equalities and Inequalities
mltype Utility Functions for MarkerList Objects
MySQLtoSQLite Load a MySQL Dump for Using with SQLite

-- N --

nbasis-method Accessing Data from CellMix Dataset
nmark Utility Functions for MarkerList Objects
nmark-method Utility Functions for MarkerList Objects
nmark-methods Utility Functions for MarkerList Objects
nmf Accessing Data in Marker Lists
nmf-method Accessing Data in Marker Lists
nmf-methods Accessing Data in Marker Lists
npure Acessing Pure or Mixed Sample Data
nuIDdecode Convert nuID to Nucleotide Sequence

-- O --

onlyRequired Checking Input and Output Data for GED Algorithms

-- P --

Palmer Palmer Dataset
profplot.MarkerList Plotting Markers
propplot Cell Type Proportion Plot
pureSamples Acessing Pure or Mixed Sample Data

-- Q --

qprog-ged Partial Gene Expression Deconvolution by Quadratic Programming
quantile.ExpressionSet Numeric Computations on ExpressionSet objects

-- R --

range-method Numeric Computations on ExpressionSet objects
refCBC Blood Sample Deconvolution
regcheck Validity Functions of Registry Fields
removeGEDMethod Register CellMix Deconvolution Methods
removeMarkerList Register CellMix MarkerLists
reorder-method Reordering Marker Lists
reverse Utility Functions for MarkerList Objects
reverse-method Utility Functions for MarkerList Objects
reverse-methods Utility Functions for MarkerList Objects
revmap-method Annotation Tools
rMarkerList Generating Marker Lists
rmarkers Generating Marker Lists
rmDuplicated Utility Functions for MarkerList Objects
rmix Generating Random Global Mixed Gene Expression Data
rowApplyBy Group Apply
rowMaxsBy Group Apply
rowMeansBy Group Apply
rowMediansBy Group Apply
rowMinsBy Group Apply
rowSumsBy Group Apply
rproportions Generating Random Cell Type Proportions
rpure Generating Random Pure Cell Type Sample

-- S --

sampleNames Extracting Feature Names
sampleNames-method Extracting Feature Names
sampleNames-methods Extracting Feature Names
sampleNames<- Extracting Feature Names
sampleNames<--method Dimensions in ExpressionMix Objects
sampleNames<--methods Extracting Feature Names
sapply-method Aplying Functions Along MarkerList Objects
scoreMarkers Extract Markers from Pure Samples.
screeplot.MarkerList Plotting Markers
selectGEDMethod Automatic Selection of Gene Expression Deconvolution Algorithms
selectMarkers Select Markers Based on Scores
selectMarkers.MarkerList Select Markers Based on Scores
selectMarkers.markerScore Select Markers Based on Scores
selectMarkers.markerScore_HSD Marker Scoring Method: Tukey Honest Significant Difference
selectMarkers.markerScore_scorem Marker scoring method: SCOREM
setAnnotation Extracting Annotation from Objects
setGEDMethod Register CellMix Deconvolution Methods
setMarkerList Register CellMix MarkerLists
show-method Factory Method for ExpressionMix Objects
show-method Class for GED Algorithms
show-method Accessing Data in Marker Lists
showData Show Data Available in an Object
showData-method Show Data Available in an Object
showData-methods Show Data Available in an Object
SLE Gene Expression from Systemic Lupus Erythematosus Patients
sort.MarkerList Reordering Marker Lists
ssFrobenius-ged Complete Gene Expression Deconvolution by Semi-Supervised NMF
ssKL-ged Complete Gene Expression Deconvolution by Semi-Supervised NMF
stack.MarkerList Converting Marker Lists into data.frames
stripchart.MarkerList Plotting Markers
subset-method Subsetting Marker Lists
subsetML Subsetting Data with MarkerList Objects
summary-method Class for Marker Gene Lists

-- T --

TDDB_HS Human Tissue Specific Genes from the TissueDistributionDB Database
TDDB_RN Rat Tissue Specific Genes from the TissueDistributionDB Database
TIGER TiGER Database
TIGER-markers TiGER - Human Tissue Specific Genes
TissueDistributionDB_HS Human Tissue Specific Genes from TissueDistributionDB
TissueDistributionDB_HS-markers Human Tissue Specific Genes from the TissueDistributionDB Database
TissueDistributionDB_RN Rat Tissue Specific Genes from TissueDistributionDB
TissueDistributionDB_RN-markers Rat Tissue Specific Genes from the TissueDistributionDB Database

-- U --

unstack.stackedMarkerList Converting Marker Lists into data.frames
userData User Data Directory

-- V --

VeryGene VeryGene Dataset
VeryGene-markers VeryGene - Marker List for Human Tissues

-- W --

wpure Acessing Pure or Mixed Sample Data

-- misc --

.atrack-method Heatmap Annotation Track for MarkerList Objects
.csSAM Cell-specific Differential Expression with csSAM
.DollarNames-method Auto-completion for 'ExpressionMix' objects
.DSAproportions Digital Sorting Algorithm: Proportion Estimation Method
.mAbbas Optimised Set of Marker Genes for Immune Cells
.mHaemAtlas HaemAtlas Marker List for Immune Cells - Watkins et al. (2009)
.mIRIS Marker Genes for Immune Cells (IRIS)
.mTDDB_HS Human Tissue Specific Genes from the TissueDistributionDB Database
.mTDDB_RN Rat Tissue Specific Genes from the TissueDistributionDB Database
.mTIGER TiGER - Human Tissue Specific Genes
[-method Subsetting ExpressionMix Objects
[-method Subsetting Marker Lists