filterCategory: Filter Ct values based on their feature categories.

Description Usage Arguments Value Author(s) See Also Examples

View source: R/filterCategory.R

Description

Ct values corresponding to selected feature categories will be replaced by NA. Generally, the feature categories indicate how reliable the values are.

Usage

1
filterCategory(q, na.categories = c("Unreliable", "Undetermined"))

Arguments

q

a qPCRset object.

na.categories

character vector, with the name(s) of the feature categories where Ct values will be considered NA.

Value

A qPCRset object like the input, but with the selected Ct values replaced by NAs

Author(s)

Heidi Dvinge

See Also

setCategory for adjusting the categories.

Examples

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data(qPCRraw)
qPCRraw2 <- setCategory(qPCRraw, groups=NULL)
x <- filterCategory(qPCRraw2)
summary(qPCRraw)
summary(x)

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Categories after Ct.max and Ct.min filtering:
             sample1 sample2 sample3 sample4 sample5 sample6
OK               313     264     327     295     296     286
Undetermined      68     119      56      86      86      96
Unreliable         3       1       1       3       2       2
        sample1  sample2  sample3 sample4  sample5  sample6 
Min.    " 7.218" " 7.408" " 6.19" " 6.853" " 6.787" " 5.133"
1st Qu. "26.738" "28.855" "27.90" "26.964" "27.913" "27.514"
Median  "28.937" "30.994" "29.92" "29.943" "30.778" "29.931"
Mean    "29.543" "32.190" "30.35" "30.590" "30.995" "30.663"
3rd Qu. "33.323" "35.985" "32.98" "34.694" "34.702" "35.046"
Max.    "40.000" "40.000" "40.00" "40.000" "40.000" "40.000"
        sample1 sample2 sample3 sample4 sample5 sample6
Min.    "11.28" "11.57" "10.62" "11.49" "10.46" "10.46"
1st Qu. "25.97" "27.92" "26.99" "26.81" "26.97" "26.83"
Median  "27.94" "29.48" "28.98" "28.45" "28.96" "27.98"
Mean    "27.88" "29.32" "29.12" "28.51" "28.95" "28.36"
3rd Qu. "29.97" "31.91" "30.97" "30.97" "31.64" "30.95"
Max.    "35.00" "35.00" "34.99" "34.92" "34.97" "34.99"
NA's    "74"    "120"   "62"    "84"    "88"    "90"   

HTqPCR documentation built on Nov. 1, 2018, 2:23 a.m.