Imports .csv-files generated by QuantaSoft.
import_QS_files(
paths,
Ch1_is_mutation = TRUE,
annotations = NULL,
sample_annotations = NULL,
merge_wells = "none",
merge_files = FALSE
)
Character vector. Specifies which files and/or directories to
load. For directories all .csv
files within are loaded.
Logical. Control if Ch1 is used to measure presence of mutant DNA (and Ch2 for wild type DNA). If this is FALSE Ch2 is used instead (and Ch1 for wild type).
Named list or data.frame
. Annotations to be added
to all samples.
data.frame
. Similar to annotations
,
but annotations are specific to each sample. This need to include a column
"Sample", which will be used for joining.
String. Controls if wells from the same sample ("Sample") should be merged within a dataset (file). There are 4 options:
merge_wells="yes"
: Merge wells. Discards QS merged wells (e.g. "M01").
merge_wells="no"
: Do **not** merge wells. Discard QS merged wells (e.g. "M01").
merge_wells="qs"
: The merged wells from QuantaSoft (e.g. "M01") is used if these are present.
merge_wells="none"
: No merging is done.
Default if "none".
Logical. If this and merge_wells
is TRUE, samples
across files are also merged. Default is FALSE.
A data.frame
with the columns:
Name of the file imported.
Well identifier.
Sample name from QuantaSoft.
The target type for channel 1.
The target type for channel 2.
Target name from QuantaSoft.
The count of mutant only droplets.
The count of wild type only droplets.
The count of double negative droplets.
The count of double positive droplets.
The total number of droplets.
If merge_wells=TRUE
this is a string of the wells merged.
Otherwise this will be NA.
The number of wells merged.