sortSeq {Repliscope} | R Documentation |
Replication profiles for wild type and Dbf4-9myc S.cerevisiae samples
Description
Replication profiles for wild type and Dbf4-9myc samples (T7107 and T9394 strains). The cells were stained with DNA dye and sorted based on DNA content into S or G2/M phase fractions. Extracted DNA was sequenced and mapped to sacCer3 genome. Unique reads for replicating (S) and non-replicating (G2/M) samples were calculated in 1 kb genomic bins. The ratio was created by dividing 'score' values from replicating sample by non- replicating sample 'score' values, adjusted by total number of reads. The ratio values were further adjusted by multiplying them by 1.41 and 1.402 for wild type and Dbf4-9myc samples, respectively, to put the values onto biologically relevant relative copy number scale from 1 to 2. The relative copy number values were smoothed using cubic spline and compared using z score statistics.
Usage
data(sortSeq)
Format
data frame with 22696 rows and 10 variables:
- chrom
short chromosome name
- chromStart
left chromosome coordinate
- chromEnd
right chromosome coordinate
- name.rep
replicating sample name
- name.nonRep
non-replicating sample name
- ratio
ratio value in the current bin
- ratioFactor
adjustment factor used for the current ratio
- group
Group number of the current bin
- splineSmooth
Smoothed ratio value
- p.value
Significance of ratio difference between Dbf4myc and W303 samples
Source
Dbf4myc S phase sample: SRA; Dbf4myc G2 sample: SRA; W303 S sample: SRA; W303 G2 sample: SRA
References
Natsume et al. (2013) Mol Cell 50(5):661-74 (PubMed)
Examples
data(sortSeq)