Function reference • mmutilR

All functions
`check.cocoa.input()`	Check CoCoA input
`fileset.list()`	Create a list of MTX-related files
`make.cocoa()`	Counterfactual confounder adjustment for individual-level differential expression analysis
`make.pine()`	Counterfactual confounder adjustment by by Pairwise INdividual Effect matching
`make.sc.deg.data()`	Simulate single-cell MTX data for DEG analysis
`make.sc.eqtl.data()`	Simulate single-cell MTX data for eQTL analysis
`make.sc.eqtl.mosaic()`	Simulate mosaic (multi-batch) single-cell MTX data for eQTL analysis.
`pine.remove.duplicated()`	Check duplicated pairs of individuals in the matching results and take the nearest ones
`rcpp_build_sparse_mat()`	Build sparse matrix from triplets
`rcpp_mmutil_aggregate()`	Create pseudo-bulk data by aggregating columns
`rcpp_mmutil_aggregate_pairwise()`	Create pseudo-bulk data for pairwise comparisons
`rcpp_mmutil_annotate_columns()`	Annotate columns by marker feature information
`rcpp_mmutil_bbknn()`	BBKNN(Batch-balancing kNN) adjustment of SVD factors
`rcpp_mmutil_bbknn_mtx()`	BBKNN(Batch-balancing kNN)-adjusted SVD
`rcpp_mmutil_build_index()`	Create an index file for a given MTX
`rcpp_mmutil_check_index()`	Check if the index tab is valid
`rcpp_mmutil_compute_scores()`	Collect row-wise and column-wise statistics
`rcpp_mmutil_copy_selected_columns()`	Take a subset of columns and create a new MTX file-set
`rcpp_mmutil_copy_selected_rows()`	Take a subset of rows and create a new MTX file-set
`rcpp_mmutil_info()`	Just read the header information
`rcpp_mmutil_match_files()`	Match the columns of two MTX files
`rcpp_mmutil_merge_file_sets()`	Merge multiple 10x mtx file sets into one set
`rcpp_mmutil_network_topic_data()`	Construct a kNN cell-cell interaction network and identify gene topics
`rcpp_mmutil_read_columns()`	Read a subset of columns from the data matrix
`rcpp_mmutil_read_columns_sparse()`	Read a subset of columns from the data matrix
`rcpp_mmutil_read_index()`	Read an index file to R
`rcpp_mmutil_simulate_poisson()`	Simulation Poisson data based on Mu
`rcpp_mmutil_simulate_poisson_mixture()`	Simulate sparse counting data with a mixture of Poisson parameters
`rcpp_mmutil_svd()`	Approximate SVD
`rcpp_mmutil_write_mtx()`	Write down sparse matrix to the disk
`read.dense()`	A wrapper function to read a dense submatrix
`read.sparse()`	A wrapper function to read a sparse submatrix
`read.vec()`	Read a vector of string names
`safe.lm()`	Regress out covariates
`simulate_indv_eqtl()`	Simulate individual-level eQTL data
`simulate_indv_glm()`	Simulate individual-level effects by GLM
`vcat.sparse()`	A wrapper function that concatenates two files vertically
`write.sparse()`	Write matrix market file set

Reference

All functions