ucarlab/bifet

A robust statistical test for TF footprint data analyses

bifet's Issues

alpha_k value

Hi,

Would you mind telling me how I could interpret alpha_k value of the output?

Thank you so much for your help.

Best,
Shoko

Error when input peak file contains GC content zero

Hi rdbcasillas,

I revisited your input peak file and noticed that your GC content values seemed strange.

# range of GC content values in peaks
range(in1$GC)
[1] 0.000000 0.213918
# how many peaks have a GC content of 0
length(which(in1$GC == 0))
[1] 55433

I'm not sure what species your peak data originated from, but it seems strange that your max GC content is ~21% (seems low; I think the average GC content in human genomes is usually between 40-60%) and that there are 50k peaks with a GC content of exactly zero. Perhaps there were some issues in calculating GC content in your input peak file?

Either way, this is an issue the developers and I will address so that users do not encounter the same error.

For now, a quick fix can be to remove the peaks in your dataset with a GC content equal to zero:

# load input files
in1 <- readRDS("Downloads/BiFet files/input1.rds")
in2 <- readRDS("Downloads/BiFet files/input2.rds")
# identify and remove peaks in peak dataset with GC content equal to zero
id_high <- which(in1$GC > 0)
in1_sel <- in1[id_high]
res <- calculate_enrich_p(in1_sel, in2)

Please give this a try and let me know if you still get the same error!

Originally posted by @nlawlor in #1 (comment)

fasten the analysis

Hi,

Thank you for developing/maintaining a great package!

Do you think it makes sense to filter the PIQ output by the peak regions to fasten the analysis, or it would make no sense?

Thank you so much for your help.

Best,
Shoko

Error in optim(init, fn = loglik_per_TF, gr = deriv_per_TF, lower = 10^(-16), : L-BFGS-B needs finite values of 'fn' (not related to GC content)

Hi,

Thanks for making the tool,

Unfortunately I get the same error even when GC content is not equal zero.
Please download R object with input files using the link : https://drive.google.com/open?id=19HZIcR5CGBwDod-Ht0jSnHBsYynGPhJB

I should say that the file containing instances of motifs (GRmotif) is NOT a result of footprint calling but of motif scanning with FIMO. But if I understand correctly BiFET should be able to process these results as well.

Thank you in advance and regards
TIm

Originally posted by @nevelsk90 in #1 (comment)

Error in optim(init, fn = loglik_per_TF, gr = deriv_per_TF, lower = 10^(-16), : L-BFGS-B needs finite values of 'fn'

Hello,

Thanks for creating BiFET.

After creating the two GRanges objects as specified in the tutorial (only difference being that I used HINT instead of PIQ), I came across this error when running the following command.

> result <- calculate_enrich_p(input1_GR, input2_GR)
[1] "PWM 1 out of 1 PWMs"
Error in optim(init, fn = loglik_per_TF, gr = deriv_per_TF, lower = 10^(-16),  : 
  L-BFGS-B needs finite values of 'fn'

I have verified that my inputs look exactly like the inputs GRmotif and GRpeaks provided with the package. The two inputs can be downloaded from this dropbox link.

Any help is greatly appreciated. Thanks!