Read LXB files

Description

Read one or more LXB files.

Usage

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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. Set text=TRUE to return the text segment of the LXB file as well. This can be useful for debugging purposes.

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

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## Not run: 
## 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)

## End(Not run)

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