checkCountDepth.Rd
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 )
group, | a character string. Two options: sudo or docker, depending to which group the user belongs. |
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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. |
pdf with the cells counts distributions
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) }