bPeaks (version 1.2)

yeastCDS: Annotations of CDS for different yeast species

Description

Annotations of CDS for different yeast species. Data were collected (July 2013) from: Genolevures http://genolevures.org/, SGD http://www.yeastgenome.org/, CGD http://www.candidagenome.org/ databases.

Usage

data(yeastCDS)

Format

yeastCDS$Saccharomyces.cerevisiae: A table (matrix) with positions of CDS (genes) in yeast S. cerevisiae. Four columns are required (chromosome, starting position, ending position, strand (W or C), description).

Source

Data were collected (July 2013) from Genolevures http://genolevures.org/, SGD http://www.yeastgenome.org/ and CGD http://www.candidagenome.org/ databases.

Details

This R object is a list composed of multiple tables (matrices) - one for each species - with positions of CDS (genes).

References

Genolevures database http://genolevures.org/

SGD database http://www.yeastgenome.org/

CGD database http://www.candidagenome.org/

Examples

# get library
library(bPeaks)

# get data
data(yeastCDS)

# different species for wich information is available
summary(yeastCDS)
#                         Length Class      Mode     
# Debaryomyces.hansenii    31370  -none-     character
# Eremothecium.gossypii    23615  -none-     character
# Kluyveromyces.lactis     25380  -none-     character
# Pichia.sorbitophila      55875  -none-     character
# Saccharomyces.kluyveri   27790  -none-     character
# Yarrowia.lipolytica      32235  -none-     character
# Zygosaccharomyces.rouxii 24955  -none-     character
# Saccharomyces.cerevisiae     5  data.frame list     
# Candida.albicans             5  data.frame list     
# Candida.glabrata             5  data.frame list

# CDS annotations for yeast Debaryomyces hansenii
yeastCDS$Debaryomyces.hansenii[1:10,]
#      chrm     start   end     strand geneName      
# [1,] "Deha2A" "2023"  "6370"  "C"    "DEHA2A00110g"
# [2,] "Deha2A" "6587"  "7810"  "C"    "DEHA2A00132g"
# [3,] "Deha2A" "8314"  "9354"  "W"    "DEHA2A00154g"
# [4,] "Deha2A" "9632"  "9844"  "C"    "DEHA2A00176g"
# [5,] "Deha2A" "13806" "14132" "W"    "DEHA2A00198g"
# [6,] "Deha2A" "14558" "16519" "C"    "DEHA2A00220g"
# [7,] "Deha2A" "17520" "19442" "W"    "DEHA2A00242g"
# [8,] "Deha2A" "22619" "23977" "C"    "DEHA2A00264g"
# [9,] "Deha2A" "24949" "25434" "W"    "DEHA2A00286g"
#[10,] "Deha2A" "26440" "26640" "C"    "DEHA2A00308g"