dataFile: Data for use in examples for the rnaseqWrapper package

In rnaseqWrapper: Wrapper for several R packages and scripts to automate RNA-seq analysis

Description

A sample of 86 rows (from three genes) of a VarScan output, and the corrresponding fasta sequence information (read in with read.fasta).

Usage

data(varScanExample)
data(fastaExample)

Source

These are from a currently unpublished analysis, and were randomly chosen.

Examples

data(varScanExample)
head(varScanExample)

data(fastaExample)
fastaExample

Example output

Loading required package: ecodist
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: gtools
     Chrom Position Ref Var Cons.Cov.Reads1.Reads2.Freq.P.value
216 gene_A       73   C   G          G:28:5:23:82.14%:3.103E-11
217 gene_A       78   C   G            G:30:3:27:90%:4.6134E-14
218 gene_A       84   C   A         A:31:6:25:80.65%:4.9949E-12
219 gene_A       85   A   G         G:33:5:27:81.82%:2.3785E-13
220 gene_A       94   G   A         A:36:4:32:88.89%:2.0653E-16
221 gene_A       99   G   A         A:36:16:20:55.56%:2.3419E-8
    StrandFilter.R1..R1..R2..R2..pval SamplesRef SamplesHet SamplesHom
216                  Pass:0:0:0:0:1E0          0          0          0
217                  Pass:0:0:0:0:1E0          0          0          0
218                  Pass:0:0:0:0:1E0          0          0          0
219                  Pass:0:0:0:0:1E0          0          0          0
220                  Pass:0:0:0:0:1E0          0          0          0
221                  Pass:0:0:0:0:1E0          0          0          0
    SamplesNC
216        10
217        10
218        10
219        10
220        10
221        10
                                                                                       Cons.Cov.Reads1.Reads2.Freq.P.value.1
216  N:3:-:-:-:- N:6:-:-:-:- N:3:-:-:-:- N:0:-:-:-:- N:3:-:-:-:- N:2:-:-:-:- N:4:-:-:-:- N:1:-:-:-:- N:3:-:-:-:- N:3:-:-:-:-
217  N:3:-:-:-:- N:7:-:-:-:- N:3:-:-:-:- N:0:-:-:-:- N:3:-:-:-:- N:2:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:3:-:-:-:- N:3:-:-:-:-
218  N:3:-:-:-:- N:6:-:-:-:- N:3:-:-:-:- N:0:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:3:-:-:-:- N:4:-:-:-:-
219  N:3:-:-:-:- N:8:-:-:-:- N:3:-:-:-:- N:0:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:3:-:-:-:- N:4:-:-:-:-
220 N:3:-:-:-:- N:10:-:-:-:- N:3:-:-:-:- N:1:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:3:-:-:-:- N:4:-:-:-:-
221 N:3:-:-:-:- N:10:-:-:-:- N:3:-:-:-:- N:1:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:4:-:-:-:- N:2:-:-:-:- N:3:-:-:-:- N:4:-:-:-:-
$gene_A
  [1] "X" "C" "A" "T" "G" "T" "T" "T" "C" "T" "C" "T" "C" "A" "T" "C" "C" "A"
 [19] "T" "C" "C" "T" "T" "G" "C" "A" "G" "C" "T" "G" "C" "A" "G" "G" "T" "G"
 [37] "C" "C" "A" "T" "C" "A" "T" "G" "C" "A" "T" "C" "T" "C" "T" "A" "A" "C"
 [55] "A" "A" "C" "A" "T" "C" "C" "C" "T" "A" "G" "A" "T" "C" "C" "T" "T" "G"
 [73] "C" "A" "A" "T" "G" "C" "C" "T" "T" "C" "C" "C" "A" "G" "C" "T" "C" "T"
 [91] "G" "C" "T" "G" "A" "A" "A" "T" "G" "T" "A" "T" "G" "A" "G" "C" "A" "T"
[109] "G" "G" "A" "G" "T" "T" "C" "C" "C" "A" "G" "G" "C" "G" "A" "A" "C" "A"
[127] "G" "C" "A" "A" "A" "T" "T" "A" "C" "A" "A" "G" "C" "C" "C" "A" "A" "C"
[145] "A" "T" "T" "T" "G" "G" "G" "A" "C" "T" "A" "C" "G" "A" "T" "T" "T" "C"
[163] "T" "T" "G" "C" "A" "G" "T" "C" "A" "T" "T" "A" "A" "C" "A" "A" "G" "T"
[181] "G" "A" "T" "T" "A" "C" "C" "A" "A" "G" "G" "C" "G" "A" "A" "G" "C" "A"
[199] "T" "A" "T" "A" "C" "T" "T" "T" "A" "A" "G" "A" "A" "C" "T" "G" "A" "A"
[217] "C" "A" "G" "T" "T" "G" "A" "A" "G" "G" "A" "A" "G" "A" "A" "A" "T" "G"
[235] "A" "A" "G" "T" "G" "C" "T" "T" "A" "C" "T" "C" "C" "A" "G" "C" "A" "A"
[253] "G" "A" "G" "G" "T" "G" "G" "A" "T" "C" "C" "A" "C" "T" "A" "A" "C" "T"
[271] "C" "A" "A" "C" "T" "A" "G" "A" "G" "T" "T" "G" "A" "T" "C" "G" "A" "C"
[289] "A" "C" "C" "A" "T" "T" "C" "A" "C" "C" "A" "T" "C" "T" "G" "G" "G" "G"
[307] "G" "T" "G" "G" "A" "C" "C" "A" "T" "A" "T" "C" "T" "T" "T" "G" "A" "T"
[325] "A" "A" "G" "G" "A" "G" "A" "T" "G" "A" "G" "G" "G" "A" "A" "A" "T" "C"
[343] "A" "T" "G" "C" "A" "C" "A" "C" "C" "A" "T" "A" "T" "G" "G" "G" "T" "T"
[361] "A" "G" "A" "C" "A" "C" "A" "A" "G" "A" "A" "C" "A" "A" "T" "G" "A" "A"
[379] "A" "A" "A" "C" "T" "G" "G" "G" "A" "G" "T" "A" "G" "A" "G" "A" "G" "T"
[397] "A" "A" "C" "A" "T" "C" "T" "A" "T" "G" "X" "X"
attr(,"name")
[1] "gene_A"
attr(,"Annot")
[1] "> gene_A"
attr(,"class")
[1] "SeqFastadna"

$gene_B
  [1] "A" "T" "G" "A" "T" "G" "C" "T" "C" "A" "G" "C" "A" "G" "C" "G" "C" "G"
 [19] "G" "C" "T" "G" "C" "C" "A" "A" "C" "A" "T" "C" "A" "T" "A" "A" "G" "A"
 [37] "A" "C" "C" "T" "C" "T" "C" "G" "C" "T" "T" "C" "T" "C" "T" "C" "T" "C"
 [55] "C" "C" "T" "C" "T" "C" "T" "T" "C" "T" "C" "C" "T" "C" "C" "C" "T" "C"
 [73] "T" "C" "C" "C" "C" "A" "A" "A" "A" "C" "C" "C" "T" "A" "C" "C" "T" "T"
 [91] "C" "G" "T" "T" "C" "C" "C" "C" "T" "T" "C" "T" "C" "C" "T" "C" "C" "T"
[109] "C" "C" "C" "C" "A" "A" "A" "A" "C" "C" "C" "T" "A" "A" "C" "C" "C" "T"
[127] "A" "T" "C" "C" "G" "T" "G" "T" "C" "T" "C" "T" "C" "C" "T" "C" "C" "T"
[145] "C" "C" "T" "C" "C" "T" "C" "C" "C" "T" "C" "C" "C" "G" "C" "C" "A" "C"
[163] "T" "T" "C" "T" "C" "C" "G" "A" "C" "T" "G" "G" "C" "G" "A" "T" "C" "T"
[181] "C" "C" "T" "C" "T" "C" "A" "G" "C" "T" "A" "C" "C" "G" "C" "G" "C" "T"
[199] "C" "T" "C" "A" "T" "C" "C" "G" "A" "T" "C" "T" "T" "C" "T" "G" "C" "C"
[217] "G" "C" "C" "G" "T" "C" "G" "C" "C" "G" "A" "G" "C" "G" "C" "T" "T" "C"
[235] "G" "A" "A" "C" "G" "C" "C" "G" "C" "A" "T" "C" "G" "C" "C" "A" "C" "C"
[253] "A" "T" "G" "G" "C" "C" "A" "C" "T" "C" "G" "G" "A" "A" "C" "T" "C" "C"
[271] "T" "T" "C" "G" "A" "G" "A" "G" "C" "A" "T" "C" "T" "T" "G" "A" "C" "G"
[289] "C" "C" "G" "C" "T" "C" "G" "C" "C" "A" "A" "G" "C" "C" "C" "G" "G" "C"
[307] "G" "G" "T" "G" "G" "C" "G" "A" "C" "T" "T" "T" "G" "G" "G" "A" "A" "G"
[325] "T" "A" "C" "T" "A" "C" "A" "G" "C" "T" "T" "G" "C" "C" "C" "G" "C" "T"
[343] "C" "T" "C" "A" "A" "C" "G" "A" "T" "C" "C" "G" "C" "G" "G" "A" "T" "C"
[361] "G" "A" "G" "A" "A" "G" "C" "T" "T" "C" "C" "A" "T" "A" "C" "T" "C" "G"
[379] "A" "T" "C" "A" "G" "G" "A" "T" "T" "C" "T" "G" "C" "T" "G" "G" "A" "G"
[397] "C" "C" "G"
attr(,"name")
[1] "gene_B"
attr(,"Annot")
[1] "> gene_B"
attr(,"class")
[1] "SeqFastadna"

$gene_C
  [1] "T" "C" "T" "G" "A" "A" "C" "C" "A" "T" "C" "T" "G" "G" "T" "T" "C" "A"
 [19] "C" "A" "G" "G" "A" "A" "C" "A" "C" "A" "T" "G" "G" "A" "C" "A" "A" "G"
 [37] "A" "A" "A" "C" "T" "C" "T" "T" "T" "T" "T" "G" "T" "G" "G" "A" "A" "G"
 [55] "T" "C" "C" "A" "A" "C" "T" "A" "C" "C" "T" "A" "T" "A" "T" "T" "T" "G"
 [73] "G" "G" "C" "G" "G" "T" "A" "G" "G" "A" "T" "C" "A" "C" "T" "C" "T" "C"
 [91] "A" "T" "C" "A" "A" "A" "C" "C" "G" "G" "C" "T" "C" "T" "G" "G" "G" "T"
[109] "A" "A" "T" "C" "T" "C" "C" "C" "T" "A" "T" "C" "T" "A" "C" "T" "T" "T"
[127] "A" "T" "G" "T" "C" "A" "A" "T" "C" "T" "T" "C" "A" "A" "G" "T" "G" "C"
[145] "C" "C" "T" "A" "T" "T" "G" "A" "A" "G" "T" "G" "G" "T" "T" "A" "A" "C"
[163] "C" "G" "T" "A" "T" "T" "G" "A" "G" "A" "G" "A" "C" "T" "T" "C" "A" "A"
[181] "A" "G" "G" "G" "A" "T" "T" "T" "T" "C" "T" "T" "T" "G" "G" "C" "A" "A"
[199] "G" "G" "A" "A" "T" "G" "G" "A" "T" "G" "A" "G" "A" "A" "G" "A" "G" "A"
[217] "A" "A" "G" "G" "A" "T" "C" "A" "T" "C" "T" "T" "A" "T" "C" "A" "A" "A"
[235] "T" "G" "G" "A" "A" "G" "A" "A" "C" "G" "T" "T" "T" "G" "C" "C" "C" "C"
[253] "C" "X" "X"
attr(,"name")
[1] "gene_C"
attr(,"Annot")
[1] "> gene_C"
attr(,"class")
[1] "SeqFastadna"

rnaseqWrapper documentation built on May 2, 2019, 5:58 a.m.