plot_incorporation.Rd
SILAC (2-plex) label incorporation is estimated from the set of observed features (peptides or proteins). If the test sample contains cells grown in 'Heavy' media only, incorporation is simply the mean observed incorporation. If the test sample contains a mixture of 'Heavy' and 'Light', the incorporation is best calculated from the median incorporation using the corrected 'Light' intensity.
plot_incorporation(
data,
incorporation_col = "Incorporation",
corrected_col = "Incorporation.corrected",
level = "peptide",
mix = 0
)
data.frame
containing features with column 'incorporation'.
If mix>0, must also contain column 'corrected_incorporation' where incorporation
is calculated using the corrected light peptide intensity
string
. Name of the column containing incorporation values
which can be calculated with get_incorporation
.
string
Optional, but required if mix > 0. Name of the
column containing mix-corrected incorporation values which can be calculated
with get_incorporation
.
string
. Name for feature level, either 'peptide' or 'protein'.
numeric
. The 'Heavy' to 'Light' mix ratio. Default is 0, otherwise
use a number greater than 0.
Returns a list
with p
= ggplot
plot and
incorporation_estimates
= list
of incorporation estimates.