TBPpwm
(Package: seqPattern) :
Position-weight matrix for TATA-box binding protein motif
This is a matrix object representing a position-weight matrix (PWM) for TATA-box binding protein motif. The scores in the matrix correspond to log2 ratio between probability of observing base b (rows) at position i (columns) and background probability of base b. This PWM has been derived using position frequency matrix from Jaspar database. It is intended to be used as an input data in running examples from seqPattern package help pages.
This is a DNAStringSet object that contains sequence of 1000 randomly selected promoters active in 24 hpf zebrafish Danio rerio embryos. The data is taken from Nepal et al. Genome Research 2013, and represents regions flanking 400 bp upstream and 600 bp downstream of the dominant TSS detected by Cap analysis of gene expression (CAGE). It is intended to be used as an input data in running examples from seqPattern package help pages.
This is a data.frame object that contains genomic coordinates of 12078 promoters active in zebrafish Danio rerio embryos at 24 hours past fertilisation. For each promoter additional information is provided, including position of the dominant (most frequently used) TSS position, number of CAGE tags per million supporting that promoter and the interquantile width of the promoter (width of the central region containing >= 80% of the CAGE tags). The data is taken from Nepal et al. Genome Research 2013, and it is intended to be used for running examples from seqPattern package vignette.
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