fldgmPicoGreen: fldgmPicoGreen

In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries

Description

Reads Fluidigm C1 cDNA yields from fluorometric measures entered in a template Excel sheet.

Usage

fldgmPicoGreen(FILE, TEMPLATE = c("PN 100-6160", "PN 100-6260"),
  FORMAT = "long", RUN)

Arguments

FILE	A standard Excel sheet containing fluorometric measurements of Fluidigm C1 cDNA yields.
TEMPLATE	devtools::document()A template identification number.
FORMAT	Long or wide.
RUN	A string representing the run name (for instance, the serial ID of the capture array.

Details

After a C1 run, the PCR products are transferred to a 96-well plate and their concentration can be quantified by a fluorometric (PicoGreen) assay in a 384-well plate. Fluidigm provides template Excel sheets in which to paste the raw results, that calculates concentrations using the standard curve, replicates and blank wells of the 384-well-plate.

This function locates the results in the Excel sheet and returns them as a data frame. Only the templates PN 100-6260 and PN 100-6160 are supported, other templates (if any) were not tested.

Value

Returns a data frame indicating containing cDNA concentrations in nanograms per microliter for each well.

In the "long" format, the data frame has 4 columns ("well", "row", "column" and "concentration") and 96 rows, sorted by well from A01, A02, ... to H11, H12. Row names are either well names, or run and well names, separated by an underscore (‘_’).

With a "wide" format, returns a data frame with 8 rows (A to H) and 12 columns (01 to 12).

Examples

## Not run: 
# With a file called "1772-064-102.picogreen.xlsx":
fldgmPicoGreen(FILE="1772-064-102.picogreen.xlsx"

# In command line:
# Rscript -e 'smallCAGEqc::fldgmPicoGreen(FILE="1772-064-102.picogreen.xlsx", TEMPLATE="PN 100-6260", RUN="1772-064-102")

## End(Not run)

charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.