yeastCDS: Annotations of CDS for different yeast species

In bPeaks: bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes

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).

Details

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

Source

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

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"

bPeaks documentation built on May 1, 2019, 10:14 p.m.