This function executes a check on the data count-depth relationship used by SCnorm.

checkCountDepth(
group = c("sudo", "docker"),
file,
conditions = NULL,
FilterCellProportion = 0.1,
FilterExpression = 0,
ditherCounts = FALSE,
outputName,
nCores = 8
)

Arguments

group,

a character string. Two options: sudo or docker, depending to which group the user belongs.

file,

a character string indicating the path of the file. IMPORTANT: full path to the file MUST be included. Only tab delimited files are supported

conditions,

vector of condition labels, this should correspond to the columns of the un-normalized expression matrix. If not provided data is assumed to come from same condition/batch.

FilterCellProportion,

a value indicating the proportion of non-zero expression estimates required to include the genes into the evaluation. Default is .10, and will not go below a proportion which uses less than 10 total cells/samples

FilterExpression,

a value indicating exclude genes having median of non-zero expression below this threshold from count-depth plots

ditherCounts,

Setting to TRUE might improve results with UMI data, default is FALSE

outputName,

specify the path and/or name of output files.

nCores,

number of cores to use, default is detectCores() - 1.

Value

pdf with the cells counts distributions

Examples

if (FALSE) {
#UMI 3' end analysis
system("wget http://130.192.119.59/public/example_UMI.txt.zip")
unzip("example_UMI.txt.zip")
conditions=rep(1,12)
checkCountDepth(group="docker", file=paste(getwd(), "example_UMI.txt", sep="/"),
conditions=conditions, FilterCellProportion=0.1, FilterExpression=0,
ditherCounts=TRUE, outputName="example_UMI", nCores=8)

}