lxb (version 1.1)

readLxb: Read LXB files

Description

Read one or more LXB files.

Usage

readLxb(paths, filter=TRUE, text=FALSE)

Arguments

paths

character vector of patterns for relative or absolute filepaths. Missing values will be ignored.

filter

set filter=TRUE to drop reads with an invalid bead ID or which did not pass the doublet discriminator test. If filter=FALSE then all data is included in the ouput.

text

include text segment in output if TRUE.

Value

• Returns a list of LXB files read. Each item in the list may consist of a text component and a data component. The former is a vector of the values in the text segment of the LXB file, the latter is a matrix of all parameters in the LXB file where each column corresponds to one parameter.

  If text=FALSE then each item only consists of the data matrix.

  If only one LXB file was read then the first item of the list is returned instead of a list with only one item.

  The names attribute of the returned list is set to the well names, if all LXB files have names of the form XXX_B1.lxb (i.e. if they end in a letter and a number). Otherwise the file names are used.

Examples

## Read file 'name.lxb' from current directory and include all
## information about the LXB file
x <- readLxb('name.lxb', filter=FALSE, text=TRUE)
dim(x$data)
names(x$text)

## Read all LXB files from current directory
xs <- readLxb('*.lxb')
length(xs)
dim(xs[[1]])

## If the LXB files end in a letter and digit, then this can be used to
## index 'xs', e.g. to inspect the first few rows of well "C10", type:
head(xs$C10)