Description Usage Arguments Value Examples

View information content for each position of the PWM. Information content is modelled using Shannon's Entropy Model. The maximum information content is therefore log2(n), where n is the number of amino acids. Colors of Amino Acids are in accordance with the Lesk scheme.

1 2 3 |

`pwm_in` |
View a PWM provided using the buildPWM. Default = NULL |

`which_pwm` |
If pwms are input (outputs of buildPWM), a kinase name must match a name in pwms$kinase$kinase list of names. Default = NULL |

`fontsize` |
Font size to use on x and y axis. Default = 10 |

`view_pwm` |
View the PWM. Default = FALSE |

`pseudo` |
Small amount added to the PWM model, where zero's exist, to avoid log zero. Default = 0.01 |

`convert_PWM` |
pwm_in is a matrix of counts at position. TRUE will convert this matrix to a PWM. Default = FALSE |

`color_scheme` |
Which color scheme to use for Amino Acid Groups. Options are "lesk" or "shapely". Default = "shapely" |

`correction_factor` |
Number of sequences used to infer the PWM. This can be used where a small number of sequences were used to build the model and included as E_n in the Shannon's Entropy Model. Default = NULL |

Visualisation of a motif, scaled on bits and two tables. 1) pwm: corresponding to the PWM from pwm and 2) pwm_bits: corresponding to the conversion to bits.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ```
## Build PWM models from phosphositeplus data with default of minimum
## of 10 substrate sequences for building a PWM model.
data(phosphositeplus_human)
##randomly sample 1000 substrates for demonstration.
set.seed(1)
sample_pwm <- phosphositeplus_human[sample(nrow(phosphositeplus_human),
1000),]
pwms <- buildPWM(sample_pwm)
## Data frame of models built and number of sequences used to build each
## PWM model:
head(pwms$kinase)
## Will not visualise the motif
CAMK2A_motif <- viewPWM(pwm_in = pwms,
which_pwm = "CAMK2A",
view_pwm = FALSE)
# Use view_pwm = TRUE to view the motif
``` |

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