Load .sem files and meta data into a SNPEffectMatrixCollection

Usage

loadSEMCollection(
  semFiles,
  semMetaData = NULL,
  semMetaKey = "",
  semIds = NULL,
  bls = NULL
)

Arguments

semFiles: A list of paths to .sem files. Expects header of .sem files to be in format #BASELINE:{bl} where bl is the numeric baseline value. If matrix does not include baseline header, must be specified in bl.
semMetaData: A data.table with meta data on each SEM
semMetaKey: The name of a column in semData that matches the semIds in the sems list as a character. If column entries have a .sem suffix, a new column named SEM_KEY will be created without the .sem suffixes.
semIds: Unique id for the sem as a character vector in same order as sems. Defaults to semFile file name without the extension.
bls: numeric vector or baseline values for the SEMs. Overrides baseline specified in semFile header.

Value

A SNPEffectMatrix object

Examples

# write a tmp file to hold a SEM
m <- matrix(rnorm(16), nrow = 4)
colnames(m) <- c("A", "C", "G", "T")
tf <- tempfile()
write.table(m, tf, quote = FALSE, sep = "\t", row.names = FALSE)

# build a meta data table
md <- data.table::data.table(transcription_factor = c("tf1"), 
                             cell_type = c("HepG2"), 
                             sem_id = c("sem_id"))
                             
loadSEMCollection(tf, semMetaData = md, semIds = "sem_id", 
                  semMetaKey = "sem_id", bls = 1)
#> An object of class SNPEffectMatrixCollection
#> sems(1): sem_id
#> semData(3): transcription_factor, cell_type, sem_id