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Constructs PANDA gene regulatory networks from single-cell gene expression data

Source: R/scorpion.R
scorpion.Rd

Constructs gene regulatory networks from single-cell gene expression data using the PANDA (Passing Attributes between Networks for Data Assimilation) algorithm.

Usage

scorpion(
  tfMotifs = NULL,
  gexMatrix,
  ppiNet = NULL,
  computingEngine = "cpu",
  nCores = 1,
  gammaValue = 10,
  nPC = 25,
  assocMethod = "pearson",
  alphaValue = 0.1,
  hammingValue = 0.001,
  nIter = Inf,
  outNet = c("regulatory", "coregulatory", "cooperative"),
  zScaling = TRUE,
  showProgress = TRUE,
  randomizationMethod = "None",
  scaleByPresent = FALSE,
  filterExpr = FALSE
)

Arguments

tfMotifs

A motif dataset, a data.frame or a matrix containing 3 columns. Each row describes an motif associated with a transcription factor (column 1) a gene (column 2) and a score (column 3) for the motif.

gexMatrix

An expression dataset, with genes in the rows and barcodes (cells) in the columns.

ppiNet

A Protein-Protein-Interaction dataset, a data.frame or matrix containing 3 columns. Each row describes a protein-protein interaction between transcription factor 1(column 1), transcription factor 2 (column 2) and a score (column 3) for the interaction.

computingEngine

Either 'cpu' or 'gpu'

nCores

Number of processors to be used if BLAS or MPI is active.

gammaValue

Graining level of data (proportion of number of single cells in the initial dataset to the number of super-cells in the final dataset)

nPC

Number of principal components to use for construction of single-cell kNN network.

assocMethod

Association method. Must be one of 'pearson', 'spearman' or 'pcNet'.

alphaValue

Value to be used for update variable.

hammingValue

Value at which to terminate the process based on Hamming distance.

nIter

Sets the maximum number of iterations PANDA can run before exiting.

outNet

A vector containing which networks to return. Options include "regulatory", "coregulatory", "cooperative".

zScaling

Boolean to indicate use of Z-Scores in output. False will use [0,1] scale.

showProgress

Boolean to indicate printing of output for algorithm progress.

randomizationMethod

Method by which to randomize gene expression matrix. Default "None". Must be one of "None", "within.gene", "by.genes". "within.gene" randomization scrambles each row of the gene expression matrix, "by.gene" scrambles gene labels.

scaleByPresent

Boolean to indicate scaling of correlations by percentage of positive samples.

filterExpr

Boolean to indicate wheter or not to remove genes with 0 expression across all cells from the GEX input.

Value

A list of matrices describing networks achieved by convergence with PANDA algorithm.

Author

Daniel Osorio <daniecos@uio.no>

Examples

# Loading example data
data(scorpionTest)

# The structure of the data
str(scorpionTest)
#> List of 3
#>  $ gex:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
#>   .. ..@ i       : int [1:4456] 1 5 8 11 22 30 33 34 36 38 ...
#>   .. ..@ p       : int [1:81] 0 47 99 149 205 258 306 342 387 423 ...
#>   .. ..@ Dim     : int [1:2] 230 80
#>   .. ..@ Dimnames:List of 2
#>   .. .. ..$ : chr [1:230] "MS4A1" "CD79B" "CD79A" "HLA-DRA" ...
#>   .. .. ..$ : chr [1:80] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA" ...
#>   .. ..@ x       : num [1:4456] 1 1 3 1 1 4 1 5 1 1 ...
#>   .. ..@ factors : list()
#>  $ tf :'data.frame':	4485 obs. of  3 variables:
#>   ..$ tf    : chr [1:4485] "ADNP" "ADNP" "ADNP" "AEBP2" ...
#>   ..$ target: chr [1:4485] "PRF1" "TMEM40" "TNFRSF1B" "CFP" ...
#>   ..$ mor   : num [1:4485] 1 1 1 1 1 1 1 1 1 1 ...
#>  $ ppi:'data.frame':	12754 obs. of  3 variables:
#>   ..$ protein1      : chr [1:12754] "ADNP" "ADNP" "ADNP" "AEBP2" ...
#>   ..$ protein2      : chr [1:12754] "ZBTB14" "NFIA" "CDC5L" "YY1" ...
#>   ..$ combined_score: num [1:12754] 0.769 0.64 0.581 0.597 0.54 0.753 0.659 0.548 0.59 0.654 ...

# List of 3
# $ gex:Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
# .. ..@ i       : int [1:4456] 1 5 8 11 22 30 33 34 36 38 ...
# .. ..@ p       : int [1:81] 0 47 99 149 205 258 306 342 387 423 ...
# .. ..@ Dim     : int [1:2] 230 80
# .. ..@ Dimnames:List of 2
# .. .. ..$ : chr [1:230] "MS4A1" "CD79B" "CD79A" "HLA-DRA" ...
# .. .. ..$ : chr [1:80] "ATGCCAGAACGACT" "CATGGCCTGTGCAT" "GAACCTGATGAACC" "TGACTGGATTCTCA" ...
# .. ..@ x       : num [1:4456] 1 1 3 1 1 4 1 5 1 1 ...
# .. ..@ factors : list()
# $ tf :'data.frame':  4485 obs. of  3 variables:
#   ..$ tf    : chr [1:4485] "ADNP" "ADNP" "ADNP" "AEBP2" ...
# ..$ target: chr [1:4485] "PRF1" "TMEM40" "TNFRSF1B" "CFP" ...
# ..$ mor   : num [1:4485] 1 1 1 1 1 1 1 1 1 1 ...
# $ ppi:'data.frame':  12754 obs. of  3 variables:
#   ..$ X.node1       : chr [1:12754] "ADNP" "ADNP" "ADNP" "AEBP2" ...
# ..$ node2         : chr [1:12754] "ZBTB14" "NFIA" "CDC5L" "YY1" ...
# ..$ combined_score: num [1:12754] 0.769 0.64 0.581 0.597 0.54 0.753 0.659 0.548 0.59 0.654 ...

# Running SCORPION with large alphaValue for testing purposes.
scorpionOutput <- scorpion(tfMotifs = scorpionTest$tf,
                           gexMatrix = scorpionTest$gex,
                           ppiNet = scorpionTest$ppi,
                           alphaValue = 0.8)
#> 
#> -- SCORPION --------------------------------------------------------------------
#> v Initializing and validating
#> v Verified sufficient samples
#> i Normalizing networks
#> i Learning Network
#> i Using tanimoto similarity
#> Iteration 0: hamming distance = 0.73486
#> Iteration 1: hamming distance = 0.22155
#> Iteration 2: hamming distance = 0.078
#> Iteration 3: hamming distance = 0.01924
#> Iteration 4: hamming distance = 0.00414
#> Iteration 5: hamming distance = 0.00085
#> v Successfully ran SCORPION on 214 Genes and 783 TFs
#> Iteration 5: hamming distance = 0.00085

#> i Time elapsed: 2.5 seconds
#> Iteration 5: hamming distance = 0.00085


# -- SCORPION --------------------------------------------------------------------------------------
# + Initializing and validating
# + Verified sufficient samples
# i Normalizing networks
# i Learning Network
# i Using tanimoto similarity
# + Successfully ran SCORPION on 214 Genes and 783 TFs

# Structure of the output.
str(scorpionOutput)
#> List of 6
#>  $ regNet  : num [1:783, 1:214] -0.413 1.517 -1.311 0.364 -1.041 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : chr [1:783] "ADNP" "AEBP2" "AIRE" "ALX1" ...
#>   .. ..$ : chr [1:214] "ACAP1" "ACRBP" "ACSM3" "ADAR" ...
#>  $ coregNet: num [1:214, 1:214] 7.07e+06 -4.06 1.76e+01 -1.16e+01 -1.62e+01 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : chr [1:214] "ACAP1" "ACRBP" "ACSM3" "ADAR" ...
#>   .. ..$ : chr [1:214] "ACAP1" "ACRBP" "ACSM3" "ADAR" ...
#>  $ coopNet : num [1:783, 1:783] 5.65e+06 -5.16 -3.79 -3.63 2.94 ...
#>   ..- attr(*, "dimnames")=List of 2
#>   .. ..$ : chr [1:783] "ADNP" "AEBP2" "AIRE" "ALX1" ...
#>   .. ..$ : chr [1:783] "ADNP" "AEBP2" "AIRE" "ALX1" ...
#>  $ numGenes: int 214
#>  $ numTFs  : int 783
#>  $ numEdges: int 167562

# List of 6
# $ regNet  :Formal class 'dgeMatrix' [package "Matrix"] with 4 slots
# .. ..@ x       : num [1:167562] -0.413 1.517 -1.311 0.364 -1.041 ...
# .. ..@ Dim     : int [1:2] 783 214
# .. ..@ Dimnames:List of 2
# .. .. ..$ : chr [1:783] "ADNP" "AEBP2" "AIRE" "ALX1" ...
# .. .. ..$ : chr [1:214] "ACAP1" "ACRBP" "ACSM3" "ADAR" ...
# .. ..@ factors : list()
# $ coregNet:Formal class 'dgeMatrix' [package "Matrix"] with 4 slots
# .. ..@ x       : num [1:45796] 7.07e+06 -4.06 1.76e+01 -1.16e+01 -1.62e+01 ...
# .. ..@ Dim     : int [1:2] 214 214
# .. ..@ Dimnames:List of 2
# .. .. ..$ : chr [1:214] "ACAP1" "ACRBP" "ACSM3" "ADAR" ...
# .. .. ..$ : chr [1:214] "ACAP1" "ACRBP" "ACSM3" "ADAR" ...
# .. ..@ factors : list()
# $ coopNet :Formal class 'dgeMatrix' [package "Matrix"] with 4 slots
# .. ..@ x       : num [1:613089] 5.65e+06 -5.16 -3.79 -3.63 2.94 ...
# .. ..@ Dim     : int [1:2] 783 783
# .. ..@ Dimnames:List of 2
# .. .. ..$ : chr [1:783] "ADNP" "AEBP2" "AIRE" "ALX1" ...
# .. .. ..$ : chr [1:783] "ADNP" "AEBP2" "AIRE" "ALX1" ...
# .. ..@ factors : list()
# $ numGenes: int 214
# $ numTFs  : int 783
# $ numEdges: int 167562