COCONUT_test_data: COCONUT test data

Description Usage Format Details Source Examples

Description

A list of lists, specifically, a list of three data objects (GSEs) from the NIH GEO repository. Each has been converted from a probe matrix to a gene matrix, and subsetted to have only 10 samples (5 healthy and 5 diseased) with only 2000 genes.

Usage

1

Format

A list of lists. Within the list, each named object consists of:

genes

a numeric matrix, gene names in rows and sample IDs in columns.

pheno

a data.frame, with sample IDs in rows and phenotype variables in columns.

Details

The data all come from the NIH GEO repository, and are subsets of their respective GSE IDs.

Source

http://www.ncbi.nlm.nih.gov/geo/

Examples

1
2
3
## see help(COCONUT) for further example
data(GSEs.test)
str(GSEs.test)

Example output

List of 3
 $ GSE28750:List of 2
  ..$ pheno:'data.frame':	10 obs. of  6 variables:
  .. ..$ Title             : Factor w/ 41 levels "Control_Healthy_1",..: 1 12 14 15 16 32 34 35 36 37
  .. ..$ DiagnosisPrimary  : Factor w/ 3 levels "Healthy","Sepsis",..: 1 1 1 1 1 2 2 2 2 2
  .. ..$ Platform_id       : chr [1:10] "GPL570" "GPL570" "GPL570" "GPL570" ...
  .. ..$ AnyInfect.1yes.0no: int [1:10] 0 0 0 0 0 1 1 1 1 1
  .. ..$ Healthy0.Sepsis1  : int [1:10] 0 0 0 0 0 1 1 1 1 1
  .. ..$ SIRS0.Sepsis1     : num [1:10] NA NA NA NA NA 1 1 1 1 1
  ..$ genes:'data.frame':	2000 obs. of  10 variables:
  .. ..$ GSM712488: num [1:2000] 2.56 1.74 1.91 2.63 1.19 ...
  .. ..$ GSM712489: num [1:2000] 2.8 1.88 2 2.82 1.27 ...
  .. ..$ GSM712490: num [1:2000] 2.27 1.77 1.97 2.56 1.18 ...
  .. ..$ GSM712491: num [1:2000] 2.34 1.83 1.69 2.63 1.17 ...
  .. ..$ GSM712492: num [1:2000] 2.41 1.75 1.89 2.58 1.42 ...
  .. ..$ GSM712478: num [1:2000] 2.19 2.1 1.98 3.11 1.27 ...
  .. ..$ GSM712479: num [1:2000] 2.77 1.58 2.05 2.94 1.24 ...
  .. ..$ GSM712480: num [1:2000] 2.42 1.79 2.15 2.71 1.24 ...
  .. ..$ GSM712481: num [1:2000] 2.4 1.89 2.1 2.72 1.32 ...
  .. ..$ GSM712482: num [1:2000] 2.34 1.7 2.05 2.25 1.52 ...
 $ GSE40012:List of 2
  ..$ pheno:'data.frame':	10 obs. of  6 variables:
  .. ..$ Title             : Factor w/ 190 levels "PAXgenewholebloodbacterialpneumoniaDay_1ID=1",..: 72 75 74 67 78 12 27 1 17 24
  .. ..$ DiagnosisPrimary  : Factor w/ 3 levels "Healthy","Sepsis",..: 1 1 1 1 1 2 2 2 2 2
  .. ..$ Platform_id       : chr [1:10] "GPL6947" "GPL6947" "GPL6947" "GPL6947" ...
  .. ..$ AnyInfect.1yes.0no: int [1:10] 0 0 0 0 0 1 1 1 1 1
  .. ..$ Healthy0.Sepsis1  : int [1:10] 0 0 0 0 0 1 1 1 1 1
  .. ..$ SIRS0.Sepsis1     : num [1:10] NA NA NA NA NA 1 1 1 1 1
  ..$ genes: num [1:2000, 1:10] 4.6 3.21 4.14 2.61 3.63 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2000] "A1BG" "A2M" "A2ML1" "A4GALT" ...
  .. .. ..$ : chr [1:10] "GSM983459" "GSM983461" "GSM983463" "GSM983465" ...
 $ GSE66099:List of 2
  ..$ pheno:'data.frame':	10 obs. of  6 variables:
  .. ..$ Title             : chr [1:10] "SampleNumber:16" "SampleNumber:19" "SampleNumber:20" "SampleNumber:21" ...
  .. ..$ DiagnosisPrimary  : chr [1:10] "Healthy" "Healthy" "Healthy" "Healthy" ...
  .. ..$ Platform_id       : chr [1:10] "GPL570" "GPL570" "GPL570" "GPL570" ...
  .. ..$ AnyInfect.1yes.0no: int [1:10] 0 0 0 0 0 1 1 1 1 1
  .. ..$ Healthy0.Sepsis1  : int [1:10] 0 0 0 0 0 1 1 1 1 1
  .. ..$ SIRS0.Sepsis1     : num [1:10] NA NA NA NA NA 1 1 1 1 1
  ..$ genes:'data.frame':	2000 obs. of  10 variables:
  .. ..$ GSM102961: num [1:2000] 2.18 1.71 2.33 3.01 1.25 ...
  .. ..$ GSM102962: num [1:2000] 2.06 1.93 2.59 2.7 1.14 ...
  .. ..$ GSM102963: num [1:2000] 2.04 1.73 2.52 3.06 1.29 ...
  .. ..$ GSM102964: num [1:2000] 2.67 1.73 2.22 2.69 1.2 ...
  .. ..$ GSM102966: num [1:2000] 2.31 1.84 2.51 2.55 1.01 ...
  .. ..$ GSM102976: num [1:2000] 1.8 1.86 2.29 2.99 1.11 ...
  .. ..$ GSM102977: num [1:2000] 1.79 1.53 2.37 2.61 1.27 ...
  .. ..$ GSM102978: num [1:2000] 1.906 2.095 2.58 2.926 0.946 ...
  .. ..$ GSM102979: num [1:2000] 1.99 1.69 2.66 2.82 1.13 ...
  .. ..$ GSM102980: num [1:2000] 1.72 2 2.33 2.79 1.07 ...

COCONUT documentation built on Sept. 19, 2017, 9:05 a.m.