fullCountsSummary {twoddpcr} | R Documentation |
Returns a data frame with basic counts, the concentration of each kind of target molecule, the ratio ch1:ch2 molecules, and the fractional abundance of ch1 molecules in the overall count.
fullCountsSummary(df, ch1Label = "Mt", ch2Label = "Wt", rows = NULL, rowID = NULL, keepCols = NULL, keepColNames = NULL)
df |
A data frame with droplet count columns in one of the following formats:
|
ch1Label |
The prefix to use for the channel 1 target. Defaults to "Mt". |
ch2Label |
The prefix to use for the channel 2 target. Defaults to "Wt". |
rows |
A vector of rows (numbers or well names) to keep from the
original data frame. If set to |
rowID |
If set, this field is used as the row names. If |
keepCols |
A vector of columns to keep from |
keepColNames |
A vector of new column names for |
A data frame with
rowID
as the row names (if given);
the droplet counts per channel;
the number of ch1 and ch2 positive and negative readings;
the ch1 and ch2 concentration, copies per 20ul, and total copies per 20ul;
the ratio of ch1 to ch2 molecules; and
the fractional abundance of ch1 molecules in the overall molecule count (as a percentage).
Anthony Chiu, anthony.chiu@cruk.manchester.ac.uk
## Take a data frame with row names given by the well names. Get estimates ## for the numbers of molecules in each sample.. fullCountsSummary(KRAScounts) ## Keep only the row numbers 3, 6 and 9. fullCountsSummary(KRAScounts, rows=c(3, 6, 9)) ## Keep only the rows labelled "F03", "A04", "D04". fullCountsSummary(KRAScounts, rows=c("F03", "A04", "D04")) ## Take a data frame with a 'Well' column and do the same as above. fullCountsSummary(KRAScountsWellCol, rowID="Well") ## Keep the 'InputAmount' column. fullCountsSummary(KRAScounts, keepCols=c("InputAmount")) ## Keep the 'InputAmount' column and rename it. fullCountsSummary(KRAScounts, keepCols=c("InputAmount"), keepColNames=c("NanogramsIn"))