helper function to check the inputs passed to marker detection function
Source:R/lasso_markers.R
check_valid_input.Rd
helper function to check the inputs passed to marker detection function
Arguments
- gene_mt
A matrix contains the transcript count in each grid. Each row refers to a grid, and each column refers to a gene. The column names must be specified and refer to the genes. This can be the output from the function
get_vectors
.- cluster_mt
A matrix contains the number of cells in a specific cluster in each grid. Each row refers to a grid, and each column refers to a cluster. The column names must be specified and refer to the clusters. Please do not assign integers as column names. This can be the output from the function
get_vectors
.- sample_names
A vector specifying the names for the samples.
- n_fold
Optional. A positive number giving the number of folds used for cross validation. This parameter will pass to
cv.glmnet
to calculate a penalty term for every gene.- background
Optional. A matrix providing the background information. Each row refers to a grid, and each column refers to one category of background information. Number of rows must equal to the number of rows in
gene_mt
andcluster_mt
. Can be obtained by only providing coordinates matricescluster_info
. to functionget_vectors
.