anotaDataSet: Sample data set for anota

In anota: ANalysis Of Translational Activity (ANOTA).

Description

6 samples with data from 2 sample categories, both cytosolic (anotaDataT) and translational (anotaDataP) together with a sample class vector (anotaPhenoVec).

Usage

data(anotaDataSet)

Format

Each data matrix (anotaDataT and anotaDataP) has 1000 rows (1000 first identifiers from complete data set) and 6 columns (noAA or rich). The anotaPhenoVec vector contains the sample class of each sample and anotaDataT, anotaDataP and phenoVec follow the same order.

Source

Ingolia, NT et al. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 2009, 10;324(5924):218-23

Examples

##load data set
data(anotaDataSet)
##check dimensions
dim(anotaDataP)
head(anotaDataP)

dim(anotaDataT)
head(anotaDataT)

anotaPhenoVec

Example output

Loading required package: qvalue
[1] 1000    6
         GSM346115_fp_noaa1_quant.txt_mod GSM346116_fp_noaa2_quant.txt_mod
15S_rRNA                        6.3782307                        4.6653395
21S_rRNA                        7.2926882                        5.3467675
HRA1                            0.8559874                        0.5319497
LSR1                            3.2245779                        2.7907564
NME1                            7.4058959                        6.4561777
Q0080                           0.8559874                        0.5319497
         dataPnoAaNew GSM346111_fp_rich1_quant.txt_mod
15S_rRNA    5.4253344                        5.5175979
21S_rRNA    6.2116876                        6.2331928
HRA1        0.6431056                        0.8790089
LSR1        3.0388024                        2.2812096
NME1        6.6829288                        5.9982567
Q0080       0.6996472                        0.8790089
         GSM346114_fp_rich2_quant.txt_mod dataPrichNew
15S_rRNA                        5.0184837    5.2772658
21S_rRNA                        5.7982334    6.1349674
HRA1                            0.8244717    0.5064268
LSR1                            2.1824193    1.8253968
NME1                            5.7638400    5.8482751
Q0080                           0.8244717    1.2528095
[1] 1000    6
         GSM346120_mrna_noaa1_quant.txt_mod GSM346122_mrna_noaa2_quant.txt_mod
15S_rRNA                          5.6848584                          4.4322249
21S_rRNA                          5.3864571                          4.1034447
HRA1                              0.5289467                          0.6254599
LSR1                              5.7882936                          5.3801571
NME1                              2.9789340                          2.9757928
Q0080                             1.8000783                          1.7497408
         dataTnoAaNew GSM346117_mrna_rich1_quant.txt_mod
15S_rRNA    4.9889810                          5.2320634
21S_rRNA    4.3901108                          4.8447773
HRA1        0.5699573                          0.6810378
LSR1        5.5556551                          5.0690061
NME1        3.1508012                          3.2010190
Q0080       1.8083446                          1.5454382
         GSM346118_mrna_rich2_quant.txt_mod dataTrichNew
15S_rRNA                          4.5797043    4.8908775
21S_rRNA                          3.7893081    4.1836531
HRA1                              0.2685943    0.3686225
LSR1                              5.2394846    5.1811370
NME1                              3.1175500    3.1011090
Q0080                             2.0818500    1.7602444
[1] "noAA" "noAA" "noAA" "rich" "rich" "rich"

anota documentation built on Nov. 8, 2020, 5:46 p.m.