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xinhe-lab / ctwas

package for the causal TWAS project
https://xinhe-lab.github.io/ctwas/
MIT License
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Undefined functions #26

Closed pcarbo closed 3 months ago

pcarbo commented 3 months ago

These functions are used in various places but as far as I can tell are not defined anywhere in the package:

warning_message
read_ld_Rvar_RDS
read_weight_fusion
compute_tf_Xb
compute_tf_Xty
compute_tf_cm
compute_tf_csd
compute_tf_d
kevinlkx commented 3 months ago

thanks Peter. These should be functions used in the old version of the package. I will check and remove those.

pcarbo commented 3 months ago

In these lines, "seqnames", "start" and "end" are also undefined. Not quite sure which packages these are from.

gene_annot_gr$chrom <- seqnames(gene_annot_gr)
gene_annot_gr$start_pos <- start(gene_annot_gr)
gene_annot_gr$end_pos <- end(gene_annot_gr)
kevinlkx commented 3 months ago

those should be from GenomicRanges package. I will import that.

kevinlkx commented 3 months ago

these functions should be fixed now.