fetch: Extract Cq data

Description Usage Arguments Details Value Author(s) Examples

View source: R/fetch.R

Description

Extracts Cq data from a data frame (optionally read from a file) and (optionally) creates cqdat object.

Usage

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fetch(data=NULL,panel=NA,dir=NULL,sep="\t",skip=11,
  header=TRUE,check.names=FALSE,cq.xlim=NA,out=c(3.5,5),
  cols=NULL,vals=NULL,Rep=NA,
  colx="Chamber ID",coly="Chamber ID",colpan="Panel ID",
  colcq="Value",colh="Threshold",colfail="Call",
  funx=function(x) substr(x,6, 7),
  funy=function(x) substr(x,10,11),
  funfail=function(x) x=="Fail",h=NA,raw=FALSE)

Arguments

data

either data frame or filename.

panel

the panel number (alternatively use cols, vals and if necessary Rep).

dir

directory of file (if not working directory).

sep

if data is a filename then the field separator character (see read.table).

skip

the number of lines of the data file (excluding any header) to skip before beginning to read data.

header

logical. Whether the file or data frame contains the names of the variables as its first line.

check.names

logical. If TRUE and data is a filename then the names of the variables in the extracted data frame are checked to ensure that they are syntactically valid variable names.

cq.xlim

if NA then no panel columns are trimmed, if vector then cq.xlim[1] and cq.xlim[2] are the start and end columns for which Cq data is retained, with positive and negative counts only kept for remaining trimmed columns.

out

vector of 2 positive numbers defining distance from mean (after detrending) for excluding low and high outliers respectively.

cols

vector of indices and/or character strings identifying the panel to get the data for data (not used if pan specified).

vals

vector of indices and/or character strings (in order of cols) identifying the values taken by the data in the columns designated by cols for the desired panel (not used if panel specified).

Rep

if cols and vals reduce the data to more than 1 panel, then the Rep'th panel is used (not used if panel specified).

colx, coly, colpan, colcq, colh

integers and/or character strings identifying columns for x-location, y-location, panel number, Cq values, h, fail condition respectively.

colfail

integer and/or character string (or possibly vector of such) identifying columns used by funfail to identify negative partitions.

funx, funy

functions to extract x- and y-values from the columns specified by colx and coly.

funfail

function from entries of column(s) specified by colfail with logical as output to identify negative partitions.

h

threshold value (can also be extracted by specifying colh)

raw

logical. If FALSE data frame with x-, y-locations and Cq data is returned with no further processing (cq.xlim and out are ignored).

Details

This function creates a data frame of x-location data, y-location data and Cq values and either returns just it (if raw is TRUE) or passes it to prep which returns it within a cqdat object.

The function extracts data for a single panel, which can either be identified by the parameter panel, or by specifying vectors cols, vals and if necessary Rep.

If the values of cq.xlim are not within the range of x-location values then Cq data will be excluded, but with the associated positive and negative counts retained instead.

Value

Either a matrix of Cq data with locations (if raw is TRUE), or an object of class cqdat (by running prep).

Author(s)

Philip Wilson

Examples

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# Select panel directly. Trim data for columns 1-10 and 60-70
# (there are 70 columns). 
#Data is from Fluidigm output, so defaults are appropriate.
dat1<-fetch(Exp37a,panel=1,cq.xlim=c(11,60))

# Plot raw data
with(data.frame(fetch(Exp37a,panel=1,raw=TRUE)),plot(x,cq))

## Not run: 

# Extract data from a named tab-delimited file
dat<-fetch("dpcr.txt",sep="\t",panel=1)

# Extract data from a named comma separated values file
dat<-fetch("dpcr.csv",sep=",",panel=1)


# Select panel indirectly. Select negative partitions
# to be those with Cq coded as 999.
data(dpcr2)
dat2<-fetch(dpcr,
  cols=c("Master Mix","Sample Name","Assay Name"),
  vals=c("GE","P2A","Jiang_16S"),
  Rep=1,colfail="Cq",funfail=function(x) x==999)

## End(Not run)

edpcr documentation built on May 2, 2019, 5:22 p.m.